diff options
Diffstat (limited to 'biology')
226 files changed, 3 insertions, 453 deletions
diff --git a/biology/abyss/pkg-descr b/biology/abyss/pkg-descr index 0353f4d41b2a..39edf013e667 100644 --- a/biology/abyss/pkg-descr +++ b/biology/abyss/pkg-descr @@ -2,5 +2,3 @@ ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. - -WWW: https://www.bcgsc.ca/resources/software/abyss diff --git a/biology/ad2vcf/pkg-descr b/biology/ad2vcf/pkg-descr index 16def19e923e..b15d7c478761 100644 --- a/biology/ad2vcf/pkg-descr +++ b/biology/ad2vcf/pkg-descr @@ -1,4 +1,2 @@ ad2vcf extracts allelic depth info from a SAM stream and adds it to a corresponding single-sample VCF file. - -WWW: https://github.com/auerlab/ad2vcf diff --git a/biology/artemis/pkg-descr b/biology/artemis/pkg-descr index dc2234e3b110..3f83d5da4331 100644 --- a/biology/artemis/pkg-descr +++ b/biology/artemis/pkg-descr @@ -8,5 +8,3 @@ ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. It can open two or more sequences (and their annotations/features) together with their comparisons (usually the result of running blastn or tblastx searches). - -WWW: https://www.sanger.ac.uk/science/tools/artemis diff --git a/biology/avida/pkg-descr b/biology/avida/pkg-descr index 3c95c2b7c2ea..72e6fde30a5f 100644 --- a/biology/avida/pkg-descr +++ b/biology/avida/pkg-descr @@ -9,5 +9,3 @@ provided by the researcher. By studying this system, one can examine evolutionary adaptation, general traits of living systems (such as self-organization), and other issues pertaining to theoretical or evolutionary biology and dynamic systems. - -WWW: http://avida.devosoft.org/ diff --git a/biology/babel/pkg-descr b/biology/babel/pkg-descr index ced96ca3a9b1..709656ebd0cb 100644 --- a/biology/babel/pkg-descr +++ b/biology/babel/pkg-descr @@ -2,5 +2,3 @@ Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file. - -WWW: http://smog.com/chem/babel/ diff --git a/biology/bamtools/pkg-descr b/biology/bamtools/pkg-descr index b2ed0122cd5a..632f635d85bd 100644 --- a/biology/bamtools/pkg-descr +++ b/biology/bamtools/pkg-descr @@ -5,5 +5,3 @@ BAM is the binary alternative to the sequence alignment/map (SAM) format used for storing genetic sequence data. It uses BGZF block compression implemented on top of the standard gzip file format to provide good compression while allowing efficient random access for indexed queries. - -WWW: https://github.com/pezmaster31/bamtools diff --git a/biology/bamutil/pkg-descr b/biology/bamutil/pkg-descr index 6eb44e52fcb7..e914877c3721 100644 --- a/biology/bamutil/pkg-descr +++ b/biology/bamutil/pkg-descr @@ -2,5 +2,3 @@ Utilities for working on SAM/BAM files from The Center for Statistical Genetics at the University of Michigan School of Public Health. It includes numerous functions such as splitting, merging, trimming reads, filtering, validation, diff, etc. - -WWW: https://github.com/statgen/bamUtil diff --git a/biology/bbmap/pkg-descr b/biology/bbmap/pkg-descr index dabb59d91cb8..a4d03cccc029 100644 --- a/biology/bbmap/pkg-descr +++ b/biology/bbmap/pkg-descr @@ -2,5 +2,3 @@ This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. - -WWW: https://jgi.doe.gov/data-and-tools/bbtools/ diff --git a/biology/bcftools/pkg-descr b/biology/bcftools/pkg-descr index 1ef4040b27d7..d3bb50e44e66 100644 --- a/biology/bcftools/pkg-descr +++ b/biology/bcftools/pkg-descr @@ -2,5 +2,3 @@ BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. - -WWW: http://www.htslib.org/ diff --git a/biology/bedtools/pkg-descr b/biology/bedtools/pkg-descr index b4295c2fba7b..551c495a896c 100644 --- a/biology/bedtools/pkg-descr +++ b/biology/bedtools/pkg-descr @@ -8,5 +8,3 @@ Although each individual utility is designed to do a relatively simple task, e.g., intersect two interval files, more sophisticated analyses can be conducted by stringing together multiple bedtools operations on the command line or in shell scripts. - -WWW: http://bedtools.readthedocs.org/ diff --git a/biology/bfc/pkg-descr b/biology/bfc/pkg-descr index a2135b6a4ecc..404cbc813cb5 100644 --- a/biology/bfc/pkg-descr +++ b/biology/bfc/pkg-descr @@ -2,5 +2,3 @@ BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. - -WWW: https://github.com/lh3/bfc diff --git a/biology/bio-mocha/pkg-descr b/biology/bio-mocha/pkg-descr index cfecbffefbde..0ab93cdde40a 100644 --- a/biology/bio-mocha/pkg-descr +++ b/biology/bio-mocha/pkg-descr @@ -4,5 +4,3 @@ whole genome sequence data. It can be used both with Illumina and Affymetrix data. It can also be used for detection of germline copy number variants. Data can be prepared in usable file formats using the gtc2vcf plugin. - -WWW: https://software.broadinstitute.org/software/mocha/ diff --git a/biology/bioawk/pkg-descr b/biology/bioawk/pkg-descr index 41070de842f8..d771d7ea0a2f 100644 --- a/biology/bioawk/pkg-descr +++ b/biology/bioawk/pkg-descr @@ -4,5 +4,3 @@ VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk. - -WWW: https://github.com/lh3/bioawk diff --git a/biology/biococoa/pkg-descr b/biology/biococoa/pkg-descr index b183858c00e3..caa0525f1488 100644 --- a/biology/biococoa/pkg-descr +++ b/biology/biococoa/pkg-descr @@ -5,5 +5,3 @@ TNT files by writing only three lines of code. The framework is written in Cocoa (Objective-C). LICENSE: LGPL2 or later - -WWW: http://bioinformatics.org/biococoa/ diff --git a/biology/biolibc-tools/pkg-descr b/biology/biolibc-tools/pkg-descr index 0eed7c2f7313..4eaefc55cd42 100644 --- a/biology/biolibc-tools/pkg-descr +++ b/biology/biolibc-tools/pkg-descr @@ -2,5 +2,3 @@ Biolibc-tools is a collection of simple fast, memory-efficient, programs for processing biological data. These are simple programs built on biolibc that are not complex enough to warrant a separate project. - -WWW: https://github.com/auerlab/biolibc-tools diff --git a/biology/biolibc/pkg-descr b/biology/biolibc/pkg-descr index 25ace775ec47..73004372d4b0 100644 --- a/biology/biolibc/pkg-descr +++ b/biology/biolibc/pkg-descr @@ -3,5 +3,3 @@ processing biological data. Like libc, it consists of numerous disparate, general-purpose functions which could be used by a wide variety of applications. These include functions for streaming common file formats such as SAM and VCF, string functions specific to bioinformatics, etc. - -WWW: https://github.com/auerlab/biolibc diff --git a/biology/bioparser/pkg-descr b/biology/bioparser/pkg-descr index 0f798302ad87..6955f6d2dee8 100644 --- a/biology/bioparser/pkg-descr +++ b/biology/bioparser/pkg-descr @@ -1,4 +1,2 @@ Bioparser is a C++ header only parsing library for several formats in bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files. - -WWW: https://github.com/rvaser/bioparser diff --git a/biology/biosig/pkg-descr b/biology/biosig/pkg-descr index 5a12322fe229..f35f407e30db 100644 --- a/biology/biosig/pkg-descr +++ b/biology/biosig/pkg-descr @@ -6,5 +6,3 @@ application areas are: Neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems and sleep research. The aim of the BioSig project is to foster research in biomedical signal processing by providing open source software tools for many different applications. - -WWW: http://biosig.sourceforge.net/ diff --git a/biology/biosoup/pkg-descr b/biology/biosoup/pkg-descr index 1d88fceadbcd..3373e1e63115 100644 --- a/biology/biosoup/pkg-descr +++ b/biology/biosoup/pkg-descr @@ -1,4 +1,2 @@ Biosoup is a c++ collection of header only data structures used for storage and logging in bioinformatics tools. - -WWW: https://github.com/rvaser/biosoup diff --git a/biology/biostar-tools/pkg-descr b/biology/biostar-tools/pkg-descr index 104c8bdb5efb..eaf4acea11eb 100644 --- a/biology/biostar-tools/pkg-descr +++ b/biology/biostar-tools/pkg-descr @@ -14,5 +14,3 @@ conflicts with other packages. You can also install conda packages on FreeBSD. For details, see /usr/ports/sysutils/linux-miniconda-installer/pkg-descr - -WWW: https://www.biostarhandbook.com diff --git a/biology/bolt-lmm/pkg-descr b/biology/bolt-lmm/pkg-descr index 883572a29a08..63d52a895c54 100644 --- a/biology/bolt-lmm/pkg-descr +++ b/biology/bolt-lmm/pkg-descr @@ -2,5 +2,3 @@ The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations). - -WWW: https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ diff --git a/biology/bowtie/pkg-descr b/biology/bowtie/pkg-descr index 03d1a2c4269f..79b1d218f585 100644 --- a/biology/bowtie/pkg-descr +++ b/biology/bowtie/pkg-descr @@ -1,5 +1,3 @@ Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. - -WWW: http://bowtie-bio.sourceforge.net/index.shtml diff --git a/biology/bowtie2/pkg-descr b/biology/bowtie2/pkg-descr index 05ac47289c51..79b1d218f585 100644 --- a/biology/bowtie2/pkg-descr +++ b/biology/bowtie2/pkg-descr @@ -1,5 +1,3 @@ Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. - -WWW: https://github.com/BenLangmead/bowtie2 diff --git a/biology/bwa/pkg-descr b/biology/bwa/pkg-descr index 031b7f19fbb2..60f539b01220 100644 --- a/biology/bwa/pkg-descr +++ b/biology/bwa/pkg-descr @@ -1,5 +1,3 @@ BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads. - -WWW: https://sourceforge.net/projects/bio-bwa/ diff --git a/biology/canu/pkg-descr b/biology/canu/pkg-descr index 9ff1c44b921b..719f42cf95ce 100644 --- a/biology/canu/pkg-descr +++ b/biology/canu/pkg-descr @@ -10,5 +10,3 @@ Canu is a hierarchical assembly pipeline which runs in four steps: Trim corrected sequences Assemble trimmed corrected sequences - -WWW: https://canu.readthedocs.io/ diff --git a/biology/cd-hit/pkg-descr b/biology/cd-hit/pkg-descr index 1ee003c9c3ba..06848d6e1511 100644 --- a/biology/cd-hit/pkg-descr +++ b/biology/cd-hit/pkg-descr @@ -1,4 +1,2 @@ CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. - -WWW: http://weizhong-lab.ucsd.edu/cd-hit/ diff --git a/biology/cdbfasta/pkg-descr b/biology/cdbfasta/pkg-descr index b2908b0cc69f..c0ef25c244ec 100644 --- a/biology/cdbfasta/pkg-descr +++ b/biology/cdbfasta/pkg-descr @@ -1,3 +1 @@ Fast indexing and retrieval of FASTA records from flat file data bases. - -WWW: https://sourceforge.net/projects/cdbfasta/ diff --git a/biology/checkm/pkg-descr b/biology/checkm/pkg-descr index a3239bad2ee7..e97d294a9794 100644 --- a/biology/checkm/pkg-descr +++ b/biology/checkm/pkg-descr @@ -8,5 +8,3 @@ the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree. - -WWW: https://ecogenomics.github.io/CheckM/ diff --git a/biology/clustal-omega/pkg-descr b/biology/clustal-omega/pkg-descr index 7c4ad1d69b44..b294b6395cf6 100644 --- a/biology/clustal-omega/pkg-descr +++ b/biology/clustal-omega/pkg-descr @@ -4,5 +4,3 @@ of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. - -WWW: http://www.clustal.org/omega/ diff --git a/biology/clustalw/pkg-descr b/biology/clustalw/pkg-descr index 0d1088f1ff0e..5d143e5c25a6 100644 --- a/biology/clustalw/pkg-descr +++ b/biology/clustalw/pkg-descr @@ -4,5 +4,3 @@ alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms. - -WWW: http://www.clustal.org/ diff --git a/biology/cufflinks/pkg-descr b/biology/cufflinks/pkg-descr index 8fbb1acb5e0b..8e9e4077606f 100644 --- a/biology/cufflinks/pkg-descr +++ b/biology/cufflinks/pkg-descr @@ -11,5 +11,3 @@ Berkeley, Steven Salzberg's computational genomics group at the Institute of Genetic Medicine at Johns Hopkins University, and Barbara Wold's lab at Caltech. The project is now maintained by Cole Trapnell's lab at the University of Washington. - -WWW: http://cole-trapnell-lab.github.io/cufflinks/ diff --git a/biology/cytoscape/pkg-descr b/biology/cytoscape/pkg-descr index 478bc554a3db..a3b6bce323dd 100644 --- a/biology/cytoscape/pkg-descr +++ b/biology/cytoscape/pkg-descr @@ -2,5 +2,3 @@ Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web. - -WWW: http://www.cytoscape.org diff --git a/biology/ddocent/pkg-descr b/biology/ddocent/pkg-descr index 84c4e96e7a14..a74299d2a8d0 100644 --- a/biology/ddocent/pkg-descr +++ b/biology/ddocent/pkg-descr @@ -3,5 +3,3 @@ any kind of RAD sequencing. If you have a reference already, dDocent can be used to call SNPs from almost any type of NGS data set. It is designed to run on Linux based machines with large memory capacity and multiple processing cores, and it can be modified for use on HPC. - -WWW: http://ddocent.com diff --git a/biology/diamond/pkg-descr b/biology/diamond/pkg-descr index c625bbcdf61e..803b9b3d4ac9 100644 --- a/biology/diamond/pkg-descr +++ b/biology/diamond/pkg-descr @@ -3,5 +3,3 @@ DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. - -WWW: http://ab.inf.uni-tuebingen.de/software/diamond/ diff --git a/biology/dsr-pdb/pkg-descr b/biology/dsr-pdb/pkg-descr index 4cc497313c13..09bf048c3180 100644 --- a/biology/dsr-pdb/pkg-descr +++ b/biology/dsr-pdb/pkg-descr @@ -8,5 +8,3 @@ protein from/to a pdb file (which must have only one chain, but can have multiple models). The second, through the PDB class can handle pdb files with multiple models and herogens (although these are just passed through and not currently interpreted). - -WWW: https://graphics.stanford.edu/~drussel/pdb/ diff --git a/biology/edlib/pkg-descr b/biology/edlib/pkg-descr index cd54c994c275..a39dcc81c330 100644 --- a/biology/edlib/pkg-descr +++ b/biology/edlib/pkg-descr @@ -1,4 +1,2 @@ A lightweight and super fast C/C++ library for sequence alignment using edit distance. - -WWW: https://github.com/Martinsos/edlib diff --git a/biology/emboss/pkg-descr b/biology/emboss/pkg-descr index 8ae8809941d5..a66f9fa69a18 100644 --- a/biology/emboss/pkg-descr +++ b/biology/emboss/pkg-descr @@ -14,5 +14,3 @@ EMBASSY packages are third party applications which have been integrated with the EMBOSS suite, but which are not included in the base EMBOSS distribution for licensing or other reasons. The EMBASSY packages live in the biology/embassy port. - -WWW: http://www.emboss.org/ diff --git a/biology/erminej/pkg-descr b/biology/erminej/pkg-descr index 94ccbf50a01b..c27870c90403 100644 --- a/biology/erminej/pkg-descr +++ b/biology/erminej/pkg-descr @@ -4,5 +4,3 @@ particular biological pathways are "doing something interesting" in an experiment that generates long lists of candidates. The software is designed to be used by biologists with little or no informatics background (but if you do, you might be interested in the CLI or the R support). - -WWW: https://erminej.msl.ubc.ca/ diff --git a/biology/exonerate/pkg-descr b/biology/exonerate/pkg-descr index 1cd652065a70..3ec226743b37 100644 --- a/biology/exonerate/pkg-descr +++ b/biology/exonerate/pkg-descr @@ -6,5 +6,3 @@ Citation: Slater, G. S. C. and Birney, E. (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31. - -WWW: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate diff --git a/biology/fasta/pkg-descr b/biology/fasta/pkg-descr index 4ed94b5e2538..93fe0f1d0e34 100644 --- a/biology/fasta/pkg-descr +++ b/biology/fasta/pkg-descr @@ -14,5 +14,3 @@ Methods in Enzymology 183:63- 98). The FASTA2 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product. - -WWW: http://fasta.bioch.virginia.edu/ diff --git a/biology/fasta3/pkg-descr b/biology/fasta3/pkg-descr index f1087103894e..5e4d95374468 100644 --- a/biology/fasta3/pkg-descr +++ b/biology/fasta3/pkg-descr @@ -13,5 +13,3 @@ Molecular Biology 132:185-219. The FASTA3 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product. - -WWW: http://fasta.bioch.virginia.edu/ diff --git a/biology/fastahack/pkg-descr b/biology/fastahack/pkg-descr index c1ca6d3c68cf..2cdc2e1cbd05 100644 --- a/biology/fastahack/pkg-descr +++ b/biology/fastahack/pkg-descr @@ -3,5 +3,3 @@ subsequences from FASTA files. The included Fasta.cpp library provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use. - -WWW: https://github.com/ekg/fastahack diff --git a/biology/fastdnaml/pkg-descr b/biology/fastdnaml/pkg-descr index 92c534eac604..f7defef9a940 100644 --- a/biology/fastdnaml/pkg-descr +++ b/biology/fastdnaml/pkg-descr @@ -6,5 +6,3 @@ fastDNAml is an attempt to solve the same problem as DNAML, but to do so faster and using less memory, so that larger trees and/or more bootstrap replicates become tractable. Much of fastDNAml is merely a recoding of the PHYLIP 3.3 DNAML program from PASCAL to C. - -WWW: http://www.life.illinois.edu/gary/programs/fastDNAml.html diff --git a/biology/fastool/pkg-descr b/biology/fastool/pkg-descr index 7743c2a7a44f..b121e863c8ba 100644 --- a/biology/fastool/pkg-descr +++ b/biology/fastool/pkg-descr @@ -1,3 +1 @@ Simple and quick FastQ and FastA tool for file reading and conversion. - -WWW: https://github.com/fstrozzi/Fastool diff --git a/biology/fastp/pkg-descr b/biology/fastp/pkg-descr index e64bd53e0e9c..e799d025d69d 100644 --- a/biology/fastp/pkg-descr +++ b/biology/fastp/pkg-descr @@ -1,5 +1,3 @@ fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. - -WWW: https://github.com/OpenGene/fastp diff --git a/biology/fastq-trim/pkg-descr b/biology/fastq-trim/pkg-descr index 1a0daef68185..0a4ad2c041bd 100644 --- a/biology/fastq-trim/pkg-descr +++ b/biology/fastq-trim/pkg-descr @@ -1,4 +1,2 @@ Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads prior to analyses such as RNA-Seq. - -WWW: https://github.com/outpaddling/Fastq-trim diff --git a/biology/fastqc/pkg-descr b/biology/fastqc/pkg-descr index d8cfc6cb88bc..63c71afebdca 100644 --- a/biology/fastqc/pkg-descr +++ b/biology/fastqc/pkg-descr @@ -3,5 +3,3 @@ sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. - -WWW: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ diff --git a/biology/fasttree/pkg-descr b/biology/fasttree/pkg-descr index c8b02a9d8466..fbc3d3f8cbdd 100644 --- a/biology/fasttree/pkg-descr +++ b/biology/fasttree/pkg-descr @@ -1,5 +1,3 @@ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. - -WWW: http://www.microbesonline.org/fasttree/ diff --git a/biology/fastx-toolkit/pkg-descr b/biology/fastx-toolkit/pkg-descr index b5adb7ef6f36..55b9642bb4b7 100644 --- a/biology/fastx-toolkit/pkg-descr +++ b/biology/fastx-toolkit/pkg-descr @@ -1,4 +1,2 @@ The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. - -WWW: http://hannonlab.cshl.edu/fastx_toolkit/ diff --git a/biology/figtree/pkg-descr b/biology/figtree/pkg-descr index 265151d06d62..be35472ba2e9 100644 --- a/biology/figtree/pkg-descr +++ b/biology/figtree/pkg-descr @@ -3,5 +3,3 @@ for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and feature-complete as a commercial program. In particular it is designed to display summarized and annotated trees produced by BEAST. - -WWW: http://tree.bio.ed.ac.uk/software/figtree/ diff --git a/biology/flash/pkg-descr b/biology/flash/pkg-descr index 65b83f1d2db6..e039a1ae76d9 100644 --- a/biology/flash/pkg-descr +++ b/biology/flash/pkg-descr @@ -5,5 +5,3 @@ the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. - -WWW: http://ccb.jhu.edu/software/FLASH/ diff --git a/biology/fluctuate/pkg-descr b/biology/fluctuate/pkg-descr index 89d9527d9536..1651c31b53d3 100644 --- a/biology/fluctuate/pkg-descr +++ b/biology/fluctuate/pkg-descr @@ -7,5 +7,3 @@ Fluctuate forms part of the Lamarc (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) suite. See: http://evolution.genetics.washington.edu/lamarc.html - -WWW: http://evolution.genetics.washington.edu/lamarc/fluctuate.html diff --git a/biology/freebayes/pkg-descr b/biology/freebayes/pkg-descr index 22f5fbd0373c..965b4e71a1bd 100644 --- a/biology/freebayes/pkg-descr +++ b/biology/freebayes/pkg-descr @@ -3,5 +3,3 @@ polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. - -WWW: https://github.com/ekg/freebayes diff --git a/biology/garlic/pkg-descr b/biology/garlic/pkg-descr index 2ba4614ce8c0..6deb75881605 100644 --- a/biology/garlic/pkg-descr +++ b/biology/garlic/pkg-descr @@ -9,5 +9,3 @@ semi-spherical, cylindrical and semi-cylindrical. The slab position and thickness are visible in a small window. Atomic bonds as well as atoms are treated as independent drawable objects. and more. - -WWW: http://www.zucic.org/garlic/ diff --git a/biology/gatk/pkg-descr b/biology/gatk/pkg-descr index 70cd73a443e4..d1c564ee7526 100644 --- a/biology/gatk/pkg-descr +++ b/biology/gatk/pkg-descr @@ -9,5 +9,3 @@ Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. - -WWW: https://gatk.broadinstitute.org/hc/en-us diff --git a/biology/gcta/pkg-descr b/biology/gcta/pkg-descr index e4933710da7b..6c177f5eb311 100644 --- a/biology/gcta/pkg-descr +++ b/biology/gcta/pkg-descr @@ -3,5 +3,3 @@ the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. - -WWW: http://cnsgenomics.com/software/gcta/index.html diff --git a/biology/gemma/pkg-descr b/biology/gemma/pkg-descr index c4f087bd11d8..9db7086ea489 100644 --- a/biology/gemma/pkg-descr +++ b/biology/gemma/pkg-descr @@ -1,5 +1,3 @@ GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. - -WWW: https://github.com/genetics-statistics/GEMMA diff --git a/biology/generand/pkg-descr b/biology/generand/pkg-descr index 9330d828888f..7de7deed616a 100644 --- a/biology/generand/pkg-descr +++ b/biology/generand/pkg-descr @@ -1,5 +1,3 @@ Generate random genomic data in FASTA/FASTQ, SAM, or VCF format, suitable for small academic examples or test inputs of arbitrary size. Output can be piped directly to programs or redirected to a file and edited to taste. - -WWW: https://github.com/auerlab/generand diff --git a/biology/gff2ps/pkg-descr b/biology/gff2ps/pkg-descr index ab2374a01ad8..f1674a0793dc 100644 --- a/biology/gff2ps/pkg-descr +++ b/biology/gff2ps/pkg-descr @@ -2,5 +2,3 @@ gff2ps is a script program developed with the aim of converting gff-formatted records into high quality one-dimensional plots in PostScript. Such plots maybe useful for comparing genomic structures and to visualizing outputs from genome annotation programs. - -WWW: http://genome.crg.es/software/gfftools/GFF2PS.html diff --git a/biology/gffread/pkg-descr b/biology/gffread/pkg-descr index 4e33e0a24e3f..def9446aacb9 100644 --- a/biology/gffread/pkg-descr +++ b/biology/gffread/pkg-descr @@ -1,4 +1,2 @@ GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more. - -WWW: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread diff --git a/biology/gmap/pkg-descr b/biology/gmap/pkg-descr index d09d51fed649..723229d591ae 100644 --- a/biology/gmap/pkg-descr +++ b/biology/gmap/pkg-descr @@ -8,5 +8,3 @@ Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing. - -WWW: http://www.gene.com/share/gmap diff --git a/biology/gperiodic/pkg-descr b/biology/gperiodic/pkg-descr index c55a21b175b2..1b658ccd0e5e 100644 --- a/biology/gperiodic/pkg-descr +++ b/biology/gperiodic/pkg-descr @@ -1,5 +1,3 @@ Gperiodic displays a periodic table of the elements, allowing you to browse through the elements, and view detailed information about each element. - -WWW: https://sourceforge.net/projects/gperiodic/ diff --git a/biology/graphlan/pkg-descr b/biology/graphlan/pkg-descr index 63604b32715c..21a7612d8fd7 100644 --- a/biology/graphlan/pkg-descr +++ b/biology/graphlan/pkg-descr @@ -2,5 +2,3 @@ GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. - -WWW: https://bitbucket.org/nsegata/graphlan/wiki/Home diff --git a/biology/groopm/pkg-descr b/biology/groopm/pkg-descr index 969de4b5f1c1..c2b7085ec3b0 100644 --- a/biology/groopm/pkg-descr +++ b/biology/groopm/pkg-descr @@ -3,5 +3,3 @@ dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets. GroopM is largely parameter-free. Use: groopm -h for more info. - -WWW: http://ecogenomics.github.io/GroopM/ diff --git a/biology/haplohseq/pkg-descr b/biology/haplohseq/pkg-descr index 751d6d58268d..57173a7ea340 100644 --- a/biology/haplohseq/pkg-descr +++ b/biology/haplohseq/pkg-descr @@ -2,5 +2,3 @@ Haplohseq identifies regions of allelic imbalance (AI) in sequencing data obtained from impure samples where AI events exist in a potentially low proportion of cells in the sample. Input to the software includes a VCF file of genotypes and estimated phased genotypes. - -WWW: https://sites.google.com/site/integrativecancergenomics/software/haplohseq diff --git a/biology/hhsuite/pkg-descr b/biology/hhsuite/pkg-descr index 5d2df6f41513..bec4ff368560 100644 --- a/biology/hhsuite/pkg-descr +++ b/biology/hhsuite/pkg-descr @@ -4,5 +4,3 @@ factor 4 and HHblits by a factor 2 over the previous version 2.0.16. HHblits3 is ~10x faster than PSI-BLAST and ~20x faster than HMMER3. Jobs to perform HHsearch and HHblits searches with many query profile HMMs can be parallelized over cores and over servers in a cluster using OpenMP and message passing interface (MPI). - -WWW: https://github.com/soedinglab/hh-suite diff --git a/biology/hisat2/pkg-descr b/biology/hisat2/pkg-descr index c9b62e50c1b6..b2a627c14e97 100644 --- a/biology/hisat2/pkg-descr +++ b/biology/hisat2/pkg-descr @@ -1,5 +1,3 @@ HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). - -WWW: https://ccb.jhu.edu/software/hisat2/index.shtml diff --git a/biology/hmmer/pkg-descr b/biology/hmmer/pkg-descr index 1643fd56843d..85d97e06125e 100644 --- a/biology/hmmer/pkg-descr +++ b/biology/hmmer/pkg-descr @@ -6,5 +6,3 @@ Given a multiple sequence alignment as input, HMMER builds a statistical model called a "hidden Markov model" which can then be used as a query into a sequence database to find (and/or align) additional homologues of the sequence family. - -WWW: http://hmmer.org/ diff --git a/biology/htslib/pkg-descr b/biology/htslib/pkg-descr index f5684283ff81..050ad06ba93e 100644 --- a/biology/htslib/pkg-descr +++ b/biology/htslib/pkg-descr @@ -1,5 +1,3 @@ HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools. - -WWW: https://www.htslib.org/ diff --git a/biology/hyphy/pkg-descr b/biology/hyphy/pkg-descr index 6358bab50caa..ea76d24046ea 100644 --- a/biology/hyphy/pkg-descr +++ b/biology/hyphy/pkg-descr @@ -5,5 +5,3 @@ analyses. Additionally, HyPhy features support for parallel computing environments via message passing interface, MPI and it can be compiled as a shared library and called from other programming environments such as Python and R. - -WWW: http://www.hyphy.org/ diff --git a/biology/igv/pkg-descr b/biology/igv/pkg-descr index 9a9d574c4838..8630add0a5bd 100644 --- a/biology/igv/pkg-descr +++ b/biology/igv/pkg-descr @@ -2,5 +2,3 @@ The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. - -WWW: https://software.broadinstitute.org/software/igv/ diff --git a/biology/infernal/pkg-descr b/biology/infernal/pkg-descr index d964c7af6194..fe137f9c4e33 100644 --- a/biology/infernal/pkg-descr +++ b/biology/infernal/pkg-descr @@ -10,5 +10,3 @@ The Rfam database of RNA families is based on Infernal. Citation: Nawrocki & Eddy (2013) Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics 29: 2933-2935. - -WWW: http://eddylab.org/infernal/ diff --git a/biology/iolib/pkg-descr b/biology/iolib/pkg-descr index f24eca9853db..6275b2d7d589 100644 --- a/biology/iolib/pkg-descr +++ b/biology/iolib/pkg-descr @@ -3,5 +3,3 @@ general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of Unix systems, MacOS X and MS Windows. - -WWW: http://staden.sourceforge.net/ diff --git a/biology/iqtree/pkg-descr b/biology/iqtree/pkg-descr index 5e10f7dbdebe..390d55f7e9a8 100644 --- a/biology/iqtree/pkg-descr +++ b/biology/iqtree/pkg-descr @@ -11,5 +11,3 @@ As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree), a NEWICK tree file (.treefile) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL. - -WWW: http://www.iqtree.org/ diff --git a/biology/jalview/pkg-descr b/biology/jalview/pkg-descr index f8f1378b879d..5e06e95e9ced 100644 --- a/biology/jalview/pkg-descr +++ b/biology/jalview/pkg-descr @@ -18,5 +18,3 @@ o User predefined or custom colour schemes to colour alignments or groups. o Sequence feature retrieval and display on the alignment. o Print your alignment with colours and annotations. o Output alignments as HTML pages, images (PNG) or postscript (EPS). - -WWW: https://www.jalview.org diff --git a/biology/jellyfish/pkg-descr b/biology/jellyfish/pkg-descr index b1741329c04e..4b5859e3963a 100644 --- a/biology/jellyfish/pkg-descr +++ b/biology/jellyfish/pkg-descr @@ -3,5 +3,3 @@ A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. - -WWW: http://www.genome.umd.edu/jellyfish.html diff --git a/biology/kallisto/pkg-descr b/biology/kallisto/pkg-descr index 4f06ae7e4127..de9c8d8c3d2b 100644 --- a/biology/kallisto/pkg-descr +++ b/biology/kallisto/pkg-descr @@ -2,5 +2,3 @@ Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. - -WWW: https://pachterlab.github.io/kallisto/about.html diff --git a/biology/kmcp/pkg-descr b/biology/kmcp/pkg-descr index 11fa668c8755..9343e3654a75 100644 --- a/biology/kmcp/pkg-descr +++ b/biology/kmcp/pkg-descr @@ -1,5 +1,4 @@ KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping. -WWW: https://bioinf.shenwei.me/kmcp/ -WWW: https://github.com/shenwei356/kmcp +See also: https://github.com/shenwei356/kmcp diff --git a/biology/lamarc/pkg-descr b/biology/lamarc/pkg-descr index c7f535b33e3e..2cbf87342f74 100644 --- a/biology/lamarc/pkg-descr +++ b/biology/lamarc/pkg-descr @@ -3,5 +3,3 @@ Coalescence) is a package of programs for computing population parameters such as population size, population growth rate and migration rates. It does this by using likelihoods for samples of data (sequences, microsatellites, and electrophoretic polymorphisms) from populations. - -WWW: http://evolution.genetics.washington.edu/lamarc/ diff --git a/biology/libbigwig/pkg-descr b/biology/libbigwig/pkg-descr index b4f28a1aa6cb..600908d5c054 100644 --- a/biology/libbigwig/pkg-descr +++ b/biology/libbigwig/pkg-descr @@ -1,3 +1 @@ A C library for reading/parsing local and remote bigWig and bigBed files. - -WWW: https://github.com/dpryan79/libBigWig diff --git a/biology/libgff/pkg-descr b/biology/libgff/pkg-descr index 762881bedb74..4645fa1911e8 100644 --- a/biology/libgff/pkg-descr +++ b/biology/libgff/pkg-descr @@ -7,5 +7,3 @@ This library draws directly from the code in GFFRead and GCLib, and exists primarily to remove functionality (and hence code) that is unnecessary for our downstream purposes. In the future, it may be appropriate to just replace this library wholesale with GCLib. - -WWW: https://github.com/COMBINE-lab/libgff diff --git a/biology/libgtextutils/pkg-descr b/biology/libgtextutils/pkg-descr index 827b3c0e6495..477e136d3b52 100644 --- a/biology/libgtextutils/pkg-descr +++ b/biology/libgtextutils/pkg-descr @@ -1,3 +1 @@ Gordon's text utilities. - -WWW: https://github.com/agordon/libgtextutils diff --git a/biology/libneurosim/pkg-descr b/biology/libneurosim/pkg-descr index fecded8e27cd..cc54119944de 100644 --- a/biology/libneurosim/pkg-descr +++ b/biology/libneurosim/pkg-descr @@ -9,5 +9,3 @@ simulators. It is intended as an abstraction isolating both sides of the API: any simulator can use a given connection generator and a given simulator can use any library providing the ConnectionGenerator interface. It was initially developed to support the use of libcsa from NEST. - -WWW: https://github.com/INCF/libneurosim diff --git a/biology/libnuml/pkg-descr b/biology/libnuml/pkg-descr index 011a4793507b..7a0c8087057e 100644 --- a/biology/libnuml/pkg-descr +++ b/biology/libnuml/pkg-descr @@ -2,5 +2,3 @@ The Numerical Markup Language (NuML) aims to standardize the exchange and archiving of numerical results. NuML originates from the numerical aspects of the Systems Biology Results Markup Language (SBRML) with the aim of re-using it in multiple other standardization efforts. - -WWW: https://github.com/NuML/NuML diff --git a/biology/libsbml/pkg-descr b/biology/libsbml/pkg-descr index 13d0662f6114..9c0b6cc7db2e 100644 --- a/biology/libsbml/pkg-descr +++ b/biology/libsbml/pkg-descr @@ -8,6 +8,5 @@ SBML Layout proposal by Gauges, Rost, Sahle and Wegner. It's written in ISO C and C++ but can be used from all the languages listed in the right-hand box. -WWW: https://sbml.org/software/libsbml/ -WWW: https://github.com/sbmlteam/libsbml -WWW: https://synonym.caltech.edu/ +See also: https://synonym.caltech.edu/ +See also: https://github.com/sbmlteam/libsbml diff --git a/biology/libsedml/pkg-descr b/biology/libsedml/pkg-descr index 5a7f83016d46..4922781b05ad 100644 --- a/biology/libsedml/pkg-descr +++ b/biology/libsedml/pkg-descr @@ -1,4 +1,2 @@ The libSEDML project makes use of libSBML XML layer as well as code generation as starting point to produce a library for reading and writing of SED-ML models. - -WWW: https://github.com/fbergmann/libSEDML diff --git a/biology/linux-foldingathome/pkg-descr b/biology/linux-foldingathome/pkg-descr index 24805755d3ce..ce8eef79c359 100644 --- a/biology/linux-foldingathome/pkg-descr +++ b/biology/linux-foldingathome/pkg-descr @@ -13,5 +13,3 @@ proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many cancers and cancer-related syndromes. - -WWW: https://foldingathome.org/ diff --git a/biology/mafft/pkg-descr b/biology/mafft/pkg-descr index 9343adf34816..c9756bdb796d 100644 --- a/biology/mafft/pkg-descr +++ b/biology/mafft/pkg-descr @@ -12,5 +12,3 @@ Recent developments in the MAFFT multiple sequence alignment program. K. Katoh, K. Misawa, K. Kuma and T. Miyata (Nucleic Acids Res. 30: 3059-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. - -WWW: http://mafft.cbrc.jp/alignment/software/ diff --git a/biology/mapm3/pkg-descr b/biology/mapm3/pkg-descr index cf03caeaf049..d6f5a91c02f3 100644 --- a/biology/mapm3/pkg-descr +++ b/biology/mapm3/pkg-descr @@ -9,5 +9,3 @@ MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map genes controlling polygenic quantitative traits in F2 intercrosses and BC1 backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL can be found in the technical report (included with MAPMAKER/QTL). - -WWW: http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ diff --git a/biology/migrate/pkg-descr b/biology/migrate/pkg-descr index 4d341599607a..4085eebd24ff 100644 --- a/biology/migrate/pkg-descr +++ b/biology/migrate/pkg-descr @@ -2,5 +2,3 @@ Migrate estimates effective population sizes and past migration rates between two or "n" populations assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. The n-population migrate can use sequence data, microsatellite data or electrophoretic data. - -WWW: http://popgen.sc.fsu.edu/Migrate/Migrate-n.html diff --git a/biology/minimap2/pkg-descr b/biology/minimap2/pkg-descr index a9d86305f0f5..e4e8dbd749d9 100644 --- a/biology/minimap2/pkg-descr +++ b/biology/minimap2/pkg-descr @@ -14,5 +14,3 @@ sequences against a large reference database. Typical use cases include: (6) full-genome alignment between two closely related species with divergence below ~15% - -WWW: https://github.com/lh3/minimap2 diff --git a/biology/mmseqs2/pkg-descr b/biology/mmseqs2/pkg-descr index 128056f15f39..9c359124e272 100644 --- a/biology/mmseqs2/pkg-descr +++ b/biology/mmseqs2/pkg-descr @@ -6,5 +6,3 @@ and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed. - -WWW: https://github.com/soedinglab/MMseqs2 diff --git a/biology/molden/pkg-descr b/biology/molden/pkg-descr index 2b20fa8c9f98..31e2afd484d7 100644 --- a/biology/molden/pkg-descr +++ b/biology/molden/pkg-descr @@ -20,5 +20,3 @@ automatically and interactively from within Molden, as well as firing optimisation jobs. Molden has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides. - -WWW: https://www.theochem.ru.nl/molden/ diff --git a/biology/mothur/pkg-descr b/biology/mothur/pkg-descr index ab9fc4156df2..3c83103a551f 100644 --- a/biology/mothur/pkg-descr +++ b/biology/mothur/pkg-descr @@ -1,4 +1,2 @@ This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. - -WWW: https://www.mothur.org/ diff --git a/biology/mrbayes/pkg-descr b/biology/mrbayes/pkg-descr index 4f09989a08b0..c82a3fd9a25f 100644 --- a/biology/mrbayes/pkg-descr +++ b/biology/mrbayes/pkg-descr @@ -7,5 +7,3 @@ using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. - -WWW: http://nbisweden.github.io/MrBayes/ diff --git a/biology/mummer/pkg-descr b/biology/mummer/pkg-descr index f6e5ccf079fd..5df556ab4af5 100644 --- a/biology/mummer/pkg-descr +++ b/biology/mummer/pkg-descr @@ -2,5 +2,3 @@ MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. - -WWW: http://mummer.sourceforge.net/ diff --git a/biology/muscle/pkg-descr b/biology/muscle/pkg-descr index b03741e4d7fc..4b45f6b39c26 100644 --- a/biology/muscle/pkg-descr +++ b/biology/muscle/pkg-descr @@ -18,5 +18,3 @@ reduced time and space complexity. BMC Bioinformatics 5(1): 113. The NAR paper gives only a brief overview of the algorithm and implementation details. For a full discussion of the method and many of the non-default options that it offers, please see the BMC paper. - -WWW: http://www.drive5.com/muscle/ diff --git a/biology/ncbi-blast+/pkg-descr b/biology/ncbi-blast+/pkg-descr index 19fcc057c3f0..0d7c1d401bef 100644 --- a/biology/ncbi-blast+/pkg-descr +++ b/biology/ncbi-blast+/pkg-descr @@ -3,5 +3,3 @@ between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. - -WWW: http://blast.ncbi.nlm.nih.gov diff --git a/biology/ncbi-cxx-toolkit/pkg-descr b/biology/ncbi-cxx-toolkit/pkg-descr index d318cdf7ac0e..68fbd9687f3b 100644 --- a/biology/ncbi-cxx-toolkit/pkg-descr +++ b/biology/ncbi-cxx-toolkit/pkg-descr @@ -20,5 +20,3 @@ It contains: * Biological Sequences Retrieval and Processing Library * Portable FLTK and OpenGL based GUI and graphic libraries * XmlWrapp (XML parsing and handling, XSLT, XPath) - -WWW: https://ncbi.github.io/cxx-toolkit/ diff --git a/biology/ncbi-entrez-direct/pkg-descr b/biology/ncbi-entrez-direct/pkg-descr index b8215012904c..c61898844e65 100644 --- a/biology/ncbi-entrez-direct/pkg-descr +++ b/biology/ncbi-entrez-direct/pkg-descr @@ -1,5 +1,3 @@ Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. - -WWW: https://www.ncbi.nlm.nih.gov/books/NBK179288/ diff --git a/biology/ncbi-toolkit/pkg-descr b/biology/ncbi-toolkit/pkg-descr index 2c44aef32154..96b9fdeb3261 100644 --- a/biology/ncbi-toolkit/pkg-descr +++ b/biology/ncbi-toolkit/pkg-descr @@ -15,5 +15,3 @@ From the README: any changes required by our data production needs. Nontheless, many people have found it a useful and stable basis for a number of tools and applications. - -WWW: https://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html diff --git a/biology/ncbi-vdb/pkg-descr b/biology/ncbi-vdb/pkg-descr index a2adb0aa97c0..217941143274 100644 --- a/biology/ncbi-vdb/pkg-descr +++ b/biology/ncbi-vdb/pkg-descr @@ -3,5 +3,3 @@ The 'front-end' API are provided by biology/ngs-sdk port. Although the GitHub repository also contains Java and Python codes, this port currently builds only C- and C++-based libraries. - -WWW: https://github.com/ncbi/ncbi-vdb/wiki diff --git a/biology/ngs-sdk/pkg-descr b/biology/ngs-sdk/pkg-descr index b52c80174755..84ac784d4a9c 100644 --- a/biology/ngs-sdk/pkg-descr +++ b/biology/ngs-sdk/pkg-descr @@ -8,5 +8,3 @@ ncbi-vdb. The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java. - -WWW: https://github.com/ncbi/ngs diff --git a/biology/p5-AcePerl/pkg-descr b/biology/p5-AcePerl/pkg-descr index aa6d66f91abc..d1ca850aea30 100644 --- a/biology/p5-AcePerl/pkg-descr +++ b/biology/p5-AcePerl/pkg-descr @@ -1,5 +1,3 @@ AcePerl is an object-oriented Perl interface for the ACEDB genome database system. It provides functionality for connecting to remote ACEDB databases, performing queries, fetching ACE objects, and updating databases. - -WWW: https://metacpan.org/release/AcePerl diff --git a/biology/p5-Bio-ASN1-EntrezGene/pkg-descr b/biology/p5-Bio-ASN1-EntrezGene/pkg-descr index 16fb17f53f4c..ce2ab0a2d15b 100644 --- a/biology/p5-Bio-ASN1-EntrezGene/pkg-descr +++ b/biology/p5-Bio-ASN1-EntrezGene/pkg-descr @@ -7,5 +7,3 @@ gene record. The parser will report error & line number if input data does not conform to the NCBI Entrez Gene genome annotation file format. - -WWW: https://metacpan.org/release/Bio-ASN1-EntrezGene diff --git a/biology/p5-Bio-Cluster/pkg-descr b/biology/p5-Bio-Cluster/pkg-descr index dabe27a0eb2f..1a62a2db162a 100644 --- a/biology/p5-Bio-Cluster/pkg-descr +++ b/biology/p5-Bio-Cluster/pkg-descr @@ -1,4 +1,2 @@ Bio::Cluster is the BioPerl cluster modules. Classes and modules here describe the basic structure for a cluster of BioPerl objects. - -WWW: https://metacpan.org/release/Bio-Cluster diff --git a/biology/p5-Bio-Coordinate/pkg-descr b/biology/p5-Bio-Coordinate/pkg-descr index 358dc4e3a716..fd6f701519a2 100644 --- a/biology/p5-Bio-Coordinate/pkg-descr +++ b/biology/p5-Bio-Coordinate/pkg-descr @@ -1,4 +1,2 @@ Bio::Coordinate classes are used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples. - -WWW: https://metacpan.org/release/Bio-Coordinate diff --git a/biology/p5-Bio-DB-EMBL/pkg-descr b/biology/p5-Bio-DB-EMBL/pkg-descr index eabf5d8ec13f..d195a025fbef 100644 --- a/biology/p5-Bio-DB-EMBL/pkg-descr +++ b/biology/p5-Bio-DB-EMBL/pkg-descr @@ -7,5 +7,3 @@ servers in different geographical locations. The functionality of this module is inherited from Bio::DB::DBFetch which implements Bio::DB::WebDBSeqI. - -WWW: https://metacpan.org/release/Bio-DB-EMBL diff --git a/biology/p5-Bio-DB-NCBIHelper/pkg-descr b/biology/p5-Bio-DB-NCBIHelper/pkg-descr index 2fa0d08cfb54..973b2a225d39 100644 --- a/biology/p5-Bio-DB-NCBIHelper/pkg-descr +++ b/biology/p5-Bio-DB-NCBIHelper/pkg-descr @@ -2,5 +2,3 @@ Bio::DB::NCBIHelper provides a single place to setup some common methods for querying NCBI web databases. This module just centralizes the methods for constructing a URL for querying NCBI GenBank and NCBI GenPept and the common HTML stripping done in postprocess_data(). - -WWW: https://metacpan.org/release/Bio-DB-NCBIHelper diff --git a/biology/p5-Bio-Das-Lite/pkg-descr b/biology/p5-Bio-Das-Lite/pkg-descr index 6e6adfbe58e1..c445fb35a15d 100644 --- a/biology/p5-Bio-Das-Lite/pkg-descr +++ b/biology/p5-Bio-Das-Lite/pkg-descr @@ -1,4 +1,2 @@ p5-Bio-Das-Lite is an implementation of a client for the DAS protocol (XML over HTTP primarily for biological-data). - -WWW: https://metacpan.org/release/Bio-Das-Lite diff --git a/biology/p5-Bio-Das/pkg-descr b/biology/p5-Bio-Das/pkg-descr index ada0f0f0d13d..1960d71abd23 100644 --- a/biology/p5-Bio-Das/pkg-descr +++ b/biology/p5-Bio-Das/pkg-descr @@ -4,5 +4,3 @@ version 1.5. This system is described at http://biodas.org. Both unencrypted (http:) and SSL-encrypted (https:) DAS servers are sup- ported. (To run SSL, you will need IO::Socket::SSL and Net::SSLeay installed). - -WWW: https://metacpan.org/release/Bio-Das diff --git a/biology/p5-Bio-FeatureIO/pkg-descr b/biology/p5-Bio-FeatureIO/pkg-descr index 205c78e7c659..32f80cd41310 100644 --- a/biology/p5-Bio-FeatureIO/pkg-descr +++ b/biology/p5-Bio-FeatureIO/pkg-descr @@ -15,5 +15,3 @@ The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular FeatureIO object instance is configured for either input or output. A specific example of a stream object is the Bio::FeatureIO::gff object. - -WWW: https://metacpan.org/release/Bio-FeatureIO diff --git a/biology/p5-Bio-GFF3/pkg-descr b/biology/p5-Bio-GFF3/pkg-descr index a33c55b90369..5dfc77b2e7bf 100644 --- a/biology/p5-Bio-GFF3/pkg-descr +++ b/biology/p5-Bio-GFF3/pkg-descr @@ -1,5 +1,3 @@ Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files. All they do is convert back and forth between low-level Perl data structures and GFF3 text. - -WWW: https://metacpan.org/release/Bio-GFF3 diff --git a/biology/p5-Bio-Glite/pkg-descr b/biology/p5-Bio-Glite/pkg-descr index 5c45dfee7a31..5ffd64ee6945 100644 --- a/biology/p5-Bio-Glite/pkg-descr +++ b/biology/p5-Bio-Glite/pkg-descr @@ -14,5 +14,3 @@ Disadvantages includes: 1. Slower analysis speed 2. Internet connection is required 3. No other software interfaces such as the G-language Shell - -WWW: https://metacpan.org/release/Bio-Glite diff --git a/biology/p5-Bio-Graphics/pkg-descr b/biology/p5-Bio-Graphics/pkg-descr index b99d8f8ba9bf..eb638da3134b 100644 --- a/biology/p5-Bio-Graphics/pkg-descr +++ b/biology/p5-Bio-Graphics/pkg-descr @@ -1,4 +1,2 @@ p5-Bio-Graphics is a simple GD-based renderer (diagram drawer) for DNA and protein sequences. - -WWW: https://metacpan.org/release/Bio-Graphics diff --git a/biology/p5-Bio-MAGETAB/pkg-descr b/biology/p5-Bio-MAGETAB/pkg-descr index 98c165946540..9585a396b627 100644 --- a/biology/p5-Bio-MAGETAB/pkg-descr +++ b/biology/p5-Bio-MAGETAB/pkg-descr @@ -4,5 +4,3 @@ have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usability. - -WWW: https://metacpan.org/release/Bio-MAGETAB diff --git a/biology/p5-Bio-NEXUS/pkg-descr b/biology/p5-Bio-NEXUS/pkg-descr index da13bfca9d12..6a9e71108245 100644 --- a/biology/p5-Bio-NEXUS/pkg-descr +++ b/biology/p5-Bio-NEXUS/pkg-descr @@ -10,5 +10,3 @@ so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data). - -WWW: https://metacpan.org/release/Bio-NEXUS diff --git a/biology/p5-Bio-Phylo/pkg-descr b/biology/p5-Bio-Phylo/pkg-descr index 90e77b750bc5..a286fd6d9071 100644 --- a/biology/p5-Bio-Phylo/pkg-descr +++ b/biology/p5-Bio-Phylo/pkg-descr @@ -1,5 +1,3 @@ This is the base class for the Bio::Phylo package. All other modules inherit from it, the methods defined here are applicable to all. Consult the manual for usage examples: Bio::Phylo::Manual. - -WWW: https://metacpan.org/release/Bio-Phylo diff --git a/biology/p5-Bio-SCF/pkg-descr b/biology/p5-Bio-SCF/pkg-descr index 4b199e1a8c85..ee7aeeb48615 100644 --- a/biology/p5-Bio-SCF/pkg-descr +++ b/biology/p5-Bio-SCF/pkg-descr @@ -2,5 +2,3 @@ Bio::SCF module allows you to read and update (in a restricted way) SCF chromatographic sequence files. It is an interface to Roger Staden's io-lib. See the installation directions for further instructions. - -WWW: https://metacpan.org/release/Bio-SCF diff --git a/biology/p5-Bio-Variation/pkg-descr b/biology/p5-Bio-Variation/pkg-descr index 29d4524c634e..9fafea118ff1 100644 --- a/biology/p5-Bio-Variation/pkg-descr +++ b/biology/p5-Bio-Variation/pkg-descr @@ -1,3 +1 @@ Bio::Variation::* provides BioPerl variation-related functionality. - -WWW: https://metacpan.org/release/Bio-Variation diff --git a/biology/p5-BioPerl-Run/pkg-descr b/biology/p5-BioPerl-Run/pkg-descr index 4139c169c6d3..a14b7b965751 100644 --- a/biology/p5-BioPerl-Run/pkg-descr +++ b/biology/p5-BioPerl-Run/pkg-descr @@ -1,5 +1,3 @@ Bioperl-run contain modules that provides a PERL interface to various bioinformatics applications. This allows various applications to be used with common Bioperl objects. - -WWW: https://github.com/bioperl/bioperl-run diff --git a/biology/p5-BioPerl/pkg-descr b/biology/p5-BioPerl/pkg-descr index bfdb8ca5a5b9..44ac2e49cf03 100644 --- a/biology/p5-BioPerl/pkg-descr +++ b/biology/p5-BioPerl/pkg-descr @@ -7,5 +7,3 @@ genomics applications. (For an interesting aside on "How Perl saved the Human Genome Project", see http://www.bioperl.org/wiki/How_Perl_saved_human_genome) - -WWW: https://bioperl.org/ diff --git a/biology/p5-TrimGalore/pkg-descr b/biology/p5-TrimGalore/pkg-descr index 849448684845..bffcd2c6951f 100644 --- a/biology/p5-TrimGalore/pkg-descr +++ b/biology/p5-TrimGalore/pkg-descr @@ -1,4 +1,2 @@ Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. - -WWW: https://github.com/FelixKrueger/TrimGalore diff --git a/biology/p5-transdecoder/pkg-descr b/biology/p5-transdecoder/pkg-descr index a3ad8cc244d6..a24d00f8d991 100644 --- a/biology/p5-transdecoder/pkg-descr +++ b/biology/p5-transdecoder/pkg-descr @@ -2,5 +2,3 @@ TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. - -WWW: http://transdecoder.github.io/ diff --git a/biology/paml/pkg-descr b/biology/paml/pkg-descr index 68733fd977c8..068682cd2648 100644 --- a/biology/paml/pkg-descr +++ b/biology/paml/pkg-descr @@ -5,5 +5,3 @@ sequences using maximum likelihood. It is not good for tree making. It may be used to estimate parameters and test hypotheses for the study the evolutionary process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY, PhyML, or RaxML. - -WWW: http://abacus.gene.ucl.ac.uk/software/paml.html diff --git a/biology/pbbam/pkg-descr b/biology/pbbam/pkg-descr index e69614ed4778..9b3676cd4063 100644 --- a/biology/pbbam/pkg-descr +++ b/biology/pbbam/pkg-descr @@ -7,5 +7,3 @@ built around the legacy cmp.h5 format. The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities. - -WWW: https://github.com/PacificBiosciences/pbbam diff --git a/biology/pbseqan/pkg-descr b/biology/pbseqan/pkg-descr index 9600122166b3..40bf624533db 100644 --- a/biology/pbseqan/pkg-descr +++ b/biology/pbseqan/pkg-descr @@ -7,5 +7,3 @@ development team!). However PacBio only uses a small amount of the SeqAn code-base, and in addition requires a few minor fixes that didn't make it in to the initial release of SeqAn v2.0.0. Thus to minimize confusion and band-width, we will depend on this fork instead of SeqAn proper. - -WWW: https://github.com/PacificBiosciences/seqan diff --git a/biology/peak-classifier/pkg-descr b/biology/peak-classifier/pkg-descr index b123dcbc554d..9e50a43f343d 100644 --- a/biology/peak-classifier/pkg-descr +++ b/biology/peak-classifier/pkg-descr @@ -4,5 +4,3 @@ Peaks are provided in a BED file sorted by chromosome and position. The GFF must be sorted by chromosome and position, with gene-level features separated by ### tags and each gene organized into subfeatures such as transcripts and exons. This is the default for common data sources. - -WWW: https://github.com/auerlab/peak-classifier diff --git a/biology/pear-merger/pkg-descr b/biology/pear-merger/pkg-descr index d95dbeea4b26..576e16ba2d40 100644 --- a/biology/pear-merger/pkg-descr +++ b/biology/pear-merger/pkg-descr @@ -1,5 +1,3 @@ PEAR is an ultrafast, memory-efficient and highly accurate paired-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. - -WWW: http://sco.h-its.org/exelixis/web/software/pear/ diff --git a/biology/phrap/pkg-descr b/biology/phrap/pkg-descr index d8d44bb5d37c..a0348c5745b5 100644 --- a/biology/phrap/pkg-descr +++ b/biology/phrap/pkg-descr @@ -17,5 +17,3 @@ two sets of DNA sequences, and it can be used to: * compare a set of cDNA sequences to a set of cosmids * compare contigs found by two altanative assembly procedures to each other * compare phrap contigs to the final edited cosmid sequence. - -WWW: http://www.phrap.org/phredphrapconsed.html diff --git a/biology/phred/pkg-descr b/biology/phred/pkg-descr index b92feefd076a..5ca105c804d8 100644 --- a/biology/phred/pkg-descr +++ b/biology/phred/pkg-descr @@ -20,5 +20,3 @@ It contains also a data evaluation program called 'daev'. See DAEV.DOC for more information. You must obtain the tarball via e-mail to build. See the web site below. - -WWW: http://www.phrap.org/phredphrapconsed.html diff --git a/biology/phyml/pkg-descr b/biology/phyml/pkg-descr index 32223fe07dda..8b0a5802e907 100644 --- a/biology/phyml/pkg-descr +++ b/biology/phyml/pkg-descr @@ -16,5 +16,3 @@ be processed provided that they are short. Also, PhyML can handle long sequences provided that they are not numerous. With most standard personal computers, the "comfort zone" for PhyML generally lies around 3 to 500 sequences less than 2,000 character long. - -WWW: https://github.com/stephaneguindon/phyml diff --git a/biology/picard-tools/pkg-descr b/biology/picard-tools/pkg-descr index cff83afdd7ca..b17c1fa3b5bc 100644 --- a/biology/picard-tools/pkg-descr +++ b/biology/picard-tools/pkg-descr @@ -1,5 +1,3 @@ Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. - -WWW: https://broadinstitute.github.io/picard/ diff --git a/biology/plink/pkg-descr b/biology/plink/pkg-descr index ba35b2b902ee..09d911509cf2 100644 --- a/biology/plink/pkg-descr +++ b/biology/plink/pkg-descr @@ -5,5 +5,3 @@ Citation: Chang et al. (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. GigaScience 4(1) doi:10.1186/s13742-015-0047-8 - -WWW: https://www.cog-genomics.org/plink/ diff --git a/biology/pooler/pkg-descr b/biology/pooler/pkg-descr index 3eb25cec500b..0fd111dad6ee 100644 --- a/biology/pooler/pkg-descr +++ b/biology/pooler/pkg-descr @@ -18,5 +18,3 @@ Primer Pooler can: sequencing applications) * Do all of the above with degenerate primers too. - -WWW: http://ssb22.user.srcf.net/pooler/ diff --git a/biology/primer3/pkg-descr b/biology/primer3/pkg-descr index c23608aaa680..89c9d8b1c454 100644 --- a/biology/primer3/pkg-descr +++ b/biology/primer3/pkg-descr @@ -16,5 +16,3 @@ All of these criteria are user-specifiable as constraints, and some are specifiable as terms in an objective function that characterizes an optimal primer pair." - from the README file - -WWW: http://www-genome.wi.mit.edu/genome_software/other/primer3.html diff --git a/biology/prodigal/pkg-descr b/biology/prodigal/pkg-descr index 7d9eb1c4c855..d14628b6af7d 100644 --- a/biology/prodigal/pkg-descr +++ b/biology/prodigal/pkg-descr @@ -18,5 +18,3 @@ Features: translation initiation site for most genes, and can output information about every potential start site in the genome, including confidence score, RBS motif, and much more. - -WWW: https://github.com/hyattpd/Prodigal diff --git a/biology/prodigy-lig/pkg-descr b/biology/prodigy-lig/pkg-descr index e65cbf63ccb0..ecefcaaa06c8 100644 --- a/biology/prodigy-lig/pkg-descr +++ b/biology/prodigy-lig/pkg-descr @@ -1,5 +1,3 @@ PRODIGY-LIG (PROtein binDIng enerGY prediction - LIGands) is a structure-based method for the prediction of binding affinity in protein-small ligand (such as drugs or metabolites) complexes. - -WWW: https://nestor.science.uu.nl/prodigy/lig diff --git a/biology/protomol/pkg-descr b/biology/protomol/pkg-descr index 8a0b7239b89d..92424b15fadb 100644 --- a/biology/protomol/pkg-descr +++ b/biology/protomol/pkg-descr @@ -11,5 +11,3 @@ and Langevin integrators. In addition, ProtoMol has been designed to interact with VMD, a visualization engine developed by the University of Illinois that is used for displaying large biomolecular systems in three dimensions. ProtoMol is freely distributed software, and the source code is available. - -WWW: http://protomol.sourceforge.net/ diff --git a/biology/py-Genesis-PyAPI/pkg-descr b/biology/py-Genesis-PyAPI/pkg-descr index 96217993e6dc..c384cd987dc5 100644 --- a/biology/py-Genesis-PyAPI/pkg-descr +++ b/biology/py-Genesis-PyAPI/pkg-descr @@ -1,4 +1,2 @@ GenAPI is a Python API for the Genesis platform allowing to perform computations of gene expression, etc. - -WWW: https://github.com/genialis/genesis-pyapi/ diff --git a/biology/py-PySCeS/pkg-descr b/biology/py-PySCeS/pkg-descr index 72ca017a7c61..cc2e4c9e38e5 100644 --- a/biology/py-PySCeS/pkg-descr +++ b/biology/py-PySCeS/pkg-descr @@ -1,3 +1 @@ PySCeS provides a variety of tools for the analysis of cellular systems. - -WWW: http://pysces.sourceforge.net/ diff --git a/biology/py-bcbio-gff/pkg-descr b/biology/py-bcbio-gff/pkg-descr index 2eec0e8e52a5..e93a50068fca 100644 --- a/biology/py-bcbio-gff/pkg-descr +++ b/biology/py-bcbio-gff/pkg-descr @@ -1,3 +1 @@ Read and write Generic Feature Format (GFF) with Biopython integration. - -WWW: https://pypi.python.org/project/bcbio-gff/ diff --git a/biology/py-biom-format/pkg-descr b/biology/py-biom-format/pkg-descr index 41a8b5b6ca30..d3cd806a4dfd 100644 --- a/biology/py-biom-format/pkg-descr +++ b/biology/py-biom-format/pkg-descr @@ -15,5 +15,3 @@ to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. - -WWW: http://biom-format.org/ diff --git a/biology/py-biopython/pkg-descr b/biology/py-biopython/pkg-descr index 7d4c3b5de3eb..ebb159fdfce5 100644 --- a/biology/py-biopython/pkg-descr +++ b/biology/py-biopython/pkg-descr @@ -11,5 +11,3 @@ stable. This port includes optional support for Biopython-CORBA, a CORBA interface built to the BioCorba standard (http://biocorba.org/). - -WWW: https://biopython.org/ diff --git a/biology/py-bx-python/pkg-descr b/biology/py-bx-python/pkg-descr index b5bab083ebcc..c3c0ae0da04e 100644 --- a/biology/py-bx-python/pkg-descr +++ b/biology/py-bx-python/pkg-descr @@ -13,5 +13,3 @@ Data structures for working with intervals on sequences: all unset bits to be stored compactly * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation - -WWW: https://github.com/bxlab/bx-python diff --git a/biology/py-crossmap/pkg-descr b/biology/py-crossmap/pkg-descr index dfb768a40775..c66b36d63d26 100644 --- a/biology/py-crossmap/pkg-descr +++ b/biology/py-crossmap/pkg-descr @@ -2,5 +2,3 @@ CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF. - -WWW: https://pypi.python.org/pypi/crossmap diff --git a/biology/py-cutadapt/pkg-descr b/biology/py-cutadapt/pkg-descr index 43fe420cb3b5..c052f9fad30b 100644 --- a/biology/py-cutadapt/pkg-descr +++ b/biology/py-cutadapt/pkg-descr @@ -1,4 +1,2 @@ Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequences from your high-throughput sequencing reads. - -WWW: https://pypi.org/project/cutadapt/ diff --git a/biology/py-deeptools/pkg-descr b/biology/py-deeptools/pkg-descr index 35d810a014b3..bf5575be4136 100644 --- a/biology/py-deeptools/pkg-descr +++ b/biology/py-deeptools/pkg-descr @@ -5,5 +5,3 @@ different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome. - -WWW: https://github.com/deeptools/deepTools diff --git a/biology/py-deeptoolsintervals/pkg-descr b/biology/py-deeptoolsintervals/pkg-descr index 368b6da1a905..5063421f5d44 100644 --- a/biology/py-deeptoolsintervals/pkg-descr +++ b/biology/py-deeptoolsintervals/pkg-descr @@ -1,4 +1,2 @@ Deeptools_intervals is an interval tree backend designed to interface with deepTools, supporting metadata associated with each interval. - -WWW: https://github.com/deeptools/deeptools_intervals diff --git a/biology/py-dna-features-viewer/pkg-descr b/biology/py-dna-features-viewer/pkg-descr index 367dce2c930c..059126583f12 100644 --- a/biology/py-dna-features-viewer/pkg-descr +++ b/biology/py-dna-features-viewer/pkg-descr @@ -8,5 +8,3 @@ overlapping features and long labels. The library plays well with Matplotlib and Biopython, and the figures can be saved in different formats (PNG, JPEG, SVG, PDF), e.g. for report generation or LIMS interfaces. - -WWW: https://pypi.python.org/project/dna-features-viewer/ diff --git a/biology/py-dnaio/pkg-descr b/biology/py-dnaio/pkg-descr index 3ded467c3308..7235ce392860 100644 --- a/biology/py-dnaio/pkg-descr +++ b/biology/py-dnaio/pkg-descr @@ -1,5 +1,3 @@ dnaio is a Python 3 library for fast input and output of FASTQ and FASTA files. It supports paired-end data in separate files, interleaved paired-end in a single file and compression using gzip, bzip, and xz. - -WWW: https://pypi.python.org/pypi/dnaio diff --git a/biology/py-ete3/pkg-descr b/biology/py-ete3/pkg-descr index 8f86c33a6602..cff0b9f2a9e1 100644 --- a/biology/py-ete3/pkg-descr +++ b/biology/py-ete3/pkg-descr @@ -7,5 +7,3 @@ tree visualization system based on a a highly customizable tree drawing engine (PDF and SVG tree images). Although ETE is developed as a tool for phylogenetic analysis, it is also used to handle other types of hierarchical trees (i.e. clustering results). - -WWW: http://etetoolkit.org/ diff --git a/biology/py-gffutils/pkg-descr b/biology/py-gffutils/pkg-descr index 84768b7458ac..97980547ec6c 100644 --- a/biology/py-gffutils/pkg-descr +++ b/biology/py-gffutils/pkg-descr @@ -3,5 +3,3 @@ format files typically used for genomic annotations. Files are loaded into a sqlite3 database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone. - -WWW: https://github.com/daler/gffutils diff --git a/biology/py-goatools/pkg-descr b/biology/py-goatools/pkg-descr index d35285e6132e..b0988bffefe6 100644 --- a/biology/py-goatools/pkg-descr +++ b/biology/py-goatools/pkg-descr @@ -1,4 +1,2 @@ Goatools is a python library for processing Gene Ontology (GO) terms. It includes routines for processing, filtering, and visualizing GO data. - -WWW: https://pypi.python.org/pypi/goatools diff --git a/biology/py-gtfparse/pkg-descr b/biology/py-gtfparse/pkg-descr index 1138818d5e97..454372dfd2aa 100644 --- a/biology/py-gtfparse/pkg-descr +++ b/biology/py-gtfparse/pkg-descr @@ -2,5 +2,3 @@ Tools to parse files in GTF (gene transfer format). GTF is a common format to exchange large portions of, or entire genotype information. - -WWW: https://github.com/openvax/gtfparse diff --git a/biology/py-hits/pkg-descr b/biology/py-hits/pkg-descr index e1cd3e411969..aed78ca0f7fb 100644 --- a/biology/py-hits/pkg-descr +++ b/biology/py-hits/pkg-descr @@ -1,3 +1 @@ Utilities for processing high-throughput sequencing experiments. - -WWW: https://github.com/jeffhussmann/hits diff --git a/biology/py-libnuml/pkg-descr b/biology/py-libnuml/pkg-descr index a8a267cc7f76..018eab871632 100644 --- a/biology/py-libnuml/pkg-descr +++ b/biology/py-libnuml/pkg-descr @@ -4,5 +4,3 @@ The Numerical Markup Language (NuML) aims to standardize the exchange and archiving of numerical results. NuML originates from the numerical aspects of the Systems Biology Results Markup Language (SBRML) with the aim of re-using it in multiple other standardization efforts. - -WWW: https://github.com/NuML/NuML diff --git a/biology/py-libsedml/pkg-descr b/biology/py-libsedml/pkg-descr index c84d1db60018..1bdd3b3152a5 100644 --- a/biology/py-libsedml/pkg-descr +++ b/biology/py-libsedml/pkg-descr @@ -2,5 +2,3 @@ Python binding libSEDML. The libSEDML project makes use of libSBML XML layer as well as code generation as starting point to produce a library for reading and writing of SED-ML models. - -WWW: https://github.com/fbergmann/libSEDML diff --git a/biology/py-loompy/pkg-descr b/biology/py-loompy/pkg-descr index 65d3e8d7f75d..273193f149e6 100644 --- a/biology/py-loompy/pkg-descr +++ b/biology/py-loompy/pkg-descr @@ -12,5 +12,3 @@ Key features: * Automatic, on-the-fly compression * Out-of-memory data processing * Open source, BSD license - -WWW: https://loompy.org/ diff --git a/biology/py-macs2/pkg-descr b/biology/py-macs2/pkg-descr index c101167de737..0310d2e092f8 100644 --- a/biology/py-macs2/pkg-descr +++ b/biology/py-macs2/pkg-descr @@ -2,5 +2,3 @@ MACS is a tool for chromatin immunoprecipitation (ChIP) sequence analysis. MACS empirically models the length of the sequenced ChIP fragments, which tend to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. - -WWW: https://github.com/taoliu/MACS diff --git a/biology/py-mrcfile/pkg-descr b/biology/py-mrcfile/pkg-descr index 3e2b3851bfdc..8b110ad06b4c 100644 --- a/biology/py-mrcfile/pkg-descr +++ b/biology/py-mrcfile/pkg-descr @@ -1,5 +1,3 @@ mrcfile is a Python implementation of the MRC2014 file format, which is used in structural biology to store image and volume data. - -WWW: https://github.com/ccpem/mrcfile diff --git a/biology/py-multiqc/pkg-descr b/biology/py-multiqc/pkg-descr index 399f8a41c313..e4eb84c16e77 100644 --- a/biology/py-multiqc/pkg-descr +++ b/biology/py-multiqc/pkg-descr @@ -1,5 +1,3 @@ MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - -WWW: https://pypi.python.org/pypi/multiqc diff --git a/biology/py-ont-fast5-api/pkg-descr b/biology/py-ont-fast5-api/pkg-descr index e8482d387fa0..2c55efd2a52c 100644 --- a/biology/py-ont-fast5-api/pkg-descr +++ b/biology/py-ont-fast5-api/pkg-descr @@ -5,5 +5,3 @@ Nanopore .fast5 file format. It provides: o Methods to interact with and reflect the fast5 file schema o Tools to convert between multi_read and single_read formats o Tools to compress/decompress raw data in files - -WWW: https://pypi.python.org/pypi/ont_fast5_api diff --git a/biology/py-orange3-bioinformatics/pkg-descr b/biology/py-orange3-bioinformatics/pkg-descr index 1b2b2bbbda63..8979fa28157a 100644 --- a/biology/py-orange3-bioinformatics/pkg-descr +++ b/biology/py-orange3-bioinformatics/pkg-descr @@ -7,5 +7,3 @@ Orange Bioinformatics provides access to publicly available data, like GEO data sets, GO and KEGG. All features can be combined with powerful visualization, network exploration and data mining techniques from the Orange data mining framework. - -WWW: https://github.com/biolab/orange3-bioinformatics diff --git a/biology/py-orange3-single-cell/pkg-descr b/biology/py-orange3-single-cell/pkg-descr index 1716d0dae0dc..05cf4bfc5f8a 100644 --- a/biology/py-orange3-single-cell/pkg-descr +++ b/biology/py-orange3-single-cell/pkg-descr @@ -1,4 +1,2 @@ The Single Cell add-on for Orange3 adds functionality for analysis of single cell data. - -WWW: https://singlecell.biolab.si/ diff --git a/biology/py-pandas-charm/pkg-descr b/biology/py-pandas-charm/pkg-descr index 55e981af69ae..6cbddb55b898 100644 --- a/biology/py-pandas-charm/pkg-descr +++ b/biology/py-pandas-charm/pkg-descr @@ -1,5 +1,3 @@ pandas-charm is a small Python package for getting character matrices (alignments) into and out of pandas. Use this library to make pandas interoperable with BioPython and DendroPy. - -WWW: https://github.com/jmenglund/pandas-charm diff --git a/biology/py-py2bit/pkg-descr b/biology/py-py2bit/pkg-descr index f6a726605c5e..5a8cd20f56bb 100644 --- a/biology/py-py2bit/pkg-descr +++ b/biology/py-py2bit/pkg-descr @@ -1,5 +1,3 @@ py2bit is a python extension, written in C, for quick access to 2bit files for randomly accessible, packed nucleotide sequences. The extension uses lib2bit for file access. - -WWW: https://github.com/deeptools/py2bit diff --git a/biology/py-pybigwig/pkg-descr b/biology/py-pybigwig/pkg-descr index 825fb27ac6f0..165321fc6318 100644 --- a/biology/py-pybigwig/pkg-descr +++ b/biology/py-pybigwig/pkg-descr @@ -1,5 +1,3 @@ A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. This extension uses libBigWig for local and remote file access. - -WWW: https://pypi.org/project/pyBigWig/ diff --git a/biology/py-pyfaidx/pkg-descr b/biology/py-pyfaidx/pkg-descr index 7bbfc03d6bf1..95d997b87879 100644 --- a/biology/py-pyfaidx/pkg-descr +++ b/biology/py-pyfaidx/pkg-descr @@ -9,5 +9,3 @@ files using a samtools compatible index. The pyfaidx module is API compatible with the pygr seqdb module. A command-line script "faidx" is installed alongside the pyfaidx module, and facilitates complex manipulation of FASTA files without any programming knowledge. - -WWW: https://github.com/mdshw5/pyfaidx diff --git a/biology/py-pysam/pkg-descr b/biology/py-pysam/pkg-descr index 199ead088d20..6e0fa2bbf118 100644 --- a/biology/py-pysam/pkg-descr +++ b/biology/py-pysam/pkg-descr @@ -6,5 +6,3 @@ module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats. - -WWW: https://github.com/pysam-developers/pysam diff --git a/biology/py-python-libsbml/pkg-descr b/biology/py-python-libsbml/pkg-descr index 22c87a0470a3..ac9cf0c0120e 100644 --- a/biology/py-python-libsbml/pkg-descr +++ b/biology/py-python-libsbml/pkg-descr @@ -1,4 +1,2 @@ Python binding for libsbml - Systems Biology Markup Language (SBML) read/write library. - -WWW: http://sbml.org/Main_Page diff --git a/biology/py-pywgsim/pkg-descr b/biology/py-pywgsim/pkg-descr index 7853be44bcd9..05b29e3b7ce0 100644 --- a/biology/py-pywgsim/pkg-descr +++ b/biology/py-pywgsim/pkg-descr @@ -1,5 +1,3 @@ pywgsim is a modified version of the wgsim short read simulator. The code for wgsim has been modified to allow visualizing the simulated mutations as a GFF file. - -WWW: https://pypi.python.org/pypi/pywgsim diff --git a/biology/py-resdk/pkg-descr b/biology/py-resdk/pkg-descr index d256f8eb4962..adbf2525b396 100644 --- a/biology/py-resdk/pkg-descr +++ b/biology/py-resdk/pkg-descr @@ -2,5 +2,3 @@ Resolwe SDK for Python supports interaction with Resolwe server and its extension Resolwe Bioinformatics. You can use it to upload and inspect biomedical data sets, contribute annotations, run analysis, and write pipelines. - -WWW: https://github.com/genialis/resolwe-bio-py diff --git a/biology/py-scikit-bio/pkg-descr b/biology/py-scikit-bio/pkg-descr index c20bf1eab5b9..922143d7e714 100644 --- a/biology/py-scikit-bio/pkg-descr +++ b/biology/py-scikit-bio/pkg-descr @@ -1,4 +1,2 @@ scikit-bio is an open-source python package providing data structures, algorithms, and educational resources for bioinformatics. - -WWW: http://scikit-bio.org/ diff --git a/biology/py-xenaPython/pkg-descr b/biology/py-xenaPython/pkg-descr index 0dc2f282ef4f..d53216d3fe57 100644 --- a/biology/py-xenaPython/pkg-descr +++ b/biology/py-xenaPython/pkg-descr @@ -5,5 +5,3 @@ that hosts their genomic data in order to share it with others. Using this Python API and other browsers that are part of the UC Santa Cruz Xena project, it is possible to easily access a wide variety of genomic information shared by a large number of researchers. - -WWW: https://github.com/ucscXena/xenaPython diff --git a/biology/pyfasta/pkg-descr b/biology/pyfasta/pkg-descr index acd5dff1fd15..a410ba3f9c93 100644 --- a/biology/pyfasta/pkg-descr +++ b/biology/pyfasta/pkg-descr @@ -1,4 +1,2 @@ pyfasta is a python module for fast, memory-efficient, pythonic access to fasta sequence files. - -WWW: https://bitbucket.org/brentp/biostuff/src/ diff --git a/biology/python-nexus/pkg-descr b/biology/python-nexus/pkg-descr index 91c439f53f82..7ac273882581 100644 --- a/biology/python-nexus/pkg-descr +++ b/biology/python-nexus/pkg-descr @@ -1,4 +1,2 @@ python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees) reader for python. - -WWW: http://simon.net.nz/articles/python-nexus diff --git a/biology/rainbow/pkg-descr b/biology/rainbow/pkg-descr index b0d19b421df2..b05a6590462e 100644 --- a/biology/rainbow/pkg-descr +++ b/biology/rainbow/pkg-descr @@ -6,5 +6,3 @@ top-down manner. Next, along a guide tree, it iteratively merges sibling leaves in a bottom-up manner if they are similar enough. Finally, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Both optimal and suboptimal assembly results are output. - -WWW: https://sourceforge.net/projects/bio-rainbow/ diff --git a/biology/rampler/pkg-descr b/biology/rampler/pkg-descr index 4bc0e483da59..380401dbb689 100644 --- a/biology/rampler/pkg-descr +++ b/biology/rampler/pkg-descr @@ -1,5 +1,3 @@ Rampler is a standalone module for sampling genomic sequences. It supports two modes, random subsampling of sequencing data to a desired depth (given the reference length) and file splitting to desired size in bytes. - -WWW: https://github.com/rvaser/rampler diff --git a/biology/readseq/pkg-descr b/biology/readseq/pkg-descr index f07d55783e38..157d7551fcd2 100644 --- a/biology/readseq/pkg-descr +++ b/biology/readseq/pkg-descr @@ -1,5 +1,3 @@ Sequence reading library developed by the Ribosomal Database Project. It can handle genbank, embl, fasta, fastq, sff and sto files, can read from files or streams, and can handle indexing files. - -WWW: https://sourceforge.net/projects/readseq diff --git a/biology/recombine/pkg-descr b/biology/recombine/pkg-descr index e8bdda06cb5f..1db8a11e46fb 100644 --- a/biology/recombine/pkg-descr +++ b/biology/recombine/pkg-descr @@ -6,5 +6,3 @@ Recombine forms part of the Lamarc (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) suite. See: http://evolution.genetics.washington.edu/lamarc.html - -WWW: http://evolution.genetics.washington.edu/lamarc/recombine.html diff --git a/biology/ruby-bio/pkg-descr b/biology/ruby-bio/pkg-descr index 29a2d7d8ebc8..909a761f115e 100644 --- a/biology/ruby-bio/pkg-descr +++ b/biology/ruby-bio/pkg-descr @@ -1,4 +1,2 @@ BioRuby project aims to implement integrated environment for Bioinformatics by using Ruby. - -WWW: http://bioruby.org/ diff --git a/biology/rubygem-bio-executables/pkg-descr b/biology/rubygem-bio-executables/pkg-descr index 4c7b3f8dbaba..0ffcafa50bee 100644 --- a/biology/rubygem-bio-executables/pkg-descr +++ b/biology/rubygem-bio-executables/pkg-descr @@ -5,5 +5,3 @@ complexity, they were moved to this gem. This code has historically been part of the BioRuby gem, but has been split into its own gem as part of an effort to modularize BioRuby. bio-executables and many more plugins are available at biogems.info. - -WWW: https://github.com/bioruby/bioruby-executables diff --git a/biology/rubygem-bio-old-biofetch-emulator/pkg-descr b/biology/rubygem-bio-old-biofetch-emulator/pkg-descr index 6a1c467bdd30..a5cf14e342ee 100644 --- a/biology/rubygem-bio-old-biofetch-emulator/pkg-descr +++ b/biology/rubygem-bio-old-biofetch-emulator/pkg-descr @@ -3,5 +3,3 @@ discontinued BioRuby BioFetch server were still alive. It overrides methods and objects in Bio::Fetch, and if the old BioRuby BioFetch server's URL is given, it intercepts all requests and converts them into existing web services such as TogoWS, KEGG REST API, NCBI E-Utilities, and GenomeNet(genome.jp). - -WWW: https://github.com/ngoto/bioruby-old-biofetch-emulator diff --git a/biology/rubygem-bio-shell/pkg-descr b/biology/rubygem-bio-shell/pkg-descr index 29237e3aa454..9fe8adfda16f 100644 --- a/biology/rubygem-bio-shell/pkg-descr +++ b/biology/rubygem-bio-shell/pkg-descr @@ -4,5 +4,3 @@ open source bioinformatics library for Ruby. This code has historically been part of the BioRuby gem, but has been split into its own gem as part of an effort to modularize BioRuby. bio-shell and many more plugins are available at biogems.info. - -WWW: https://github.com/bioruby/bioruby-shell diff --git a/biology/rubygem-bio/pkg-descr b/biology/rubygem-bio/pkg-descr index 29a2d7d8ebc8..909a761f115e 100644 --- a/biology/rubygem-bio/pkg-descr +++ b/biology/rubygem-bio/pkg-descr @@ -1,4 +1,2 @@ BioRuby project aims to implement integrated environment for Bioinformatics by using Ruby. - -WWW: http://bioruby.org/ diff --git a/biology/sam2pairwise/pkg-descr b/biology/sam2pairwise/pkg-descr index 800de1d7998e..e3a8d5e7f3fe 100644 --- a/biology/sam2pairwise/pkg-descr +++ b/biology/sam2pairwise/pkg-descr @@ -1,4 +1,2 @@ sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read. - -WWW: https://github.com/mlafave/sam2pairwise diff --git a/biology/samtools/pkg-descr b/biology/samtools/pkg-descr index ee9b6e47fa84..23d11d1c81f7 100644 --- a/biology/samtools/pkg-descr +++ b/biology/samtools/pkg-descr @@ -1,5 +1,3 @@ Samtools implements various utilities for post-processing alignments in the SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. - -WWW: http://www.htslib.org/ diff --git a/biology/scrm/pkg-descr b/biology/scrm/pkg-descr index 99d784f7fdf9..96bb733dff22 100644 --- a/biology/scrm/pkg-descr +++ b/biology/scrm/pkg-descr @@ -4,5 +4,3 @@ the model. As coalescent simulator, it traces the ancestry of the sampled sequences backwards in time and is therefore extremely efficient. Compared to other coalescent simulators, it can simulate chromosome-scale sequences without a measureable reduction of genetic linkage between different sites. - -WWW: https://scrm.github.io/ diff --git a/biology/seaview/pkg-descr b/biology/seaview/pkg-descr index ab566028b34a..036e8d1bb3c9 100644 --- a/biology/seaview/pkg-descr +++ b/biology/seaview/pkg-descr @@ -9,5 +9,3 @@ the 'Help' button to learn how to use SeaView. Example mase files can be found at: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/ - -WWW: http://doua.prabi.fr/software/seaview diff --git a/biology/seqan-apps/pkg-descr b/biology/seqan-apps/pkg-descr index b9f4fb929dff..5cf16c6e1dac 100644 --- a/biology/seqan-apps/pkg-descr +++ b/biology/seqan-apps/pkg-descr @@ -7,5 +7,3 @@ within the SeqAn project. Among them are famous read mappers like RazerS and Yara, as well as many other tools. Some applications are packaged separately and the library can be found at biology/seqan. - -WWW: http://www.seqan.de/ diff --git a/biology/seqan/pkg-descr b/biology/seqan/pkg-descr index 890a5a4e160d..146075c6b4a0 100644 --- a/biology/seqan/pkg-descr +++ b/biology/seqan/pkg-descr @@ -5,5 +5,3 @@ focus on biological data. The library is licensed under the This port only contains the header library and API documentation. The apps are installed by biology/seqan-apps. - -WWW: https://www.seqan.de/ diff --git a/biology/seqan1/pkg-descr b/biology/seqan1/pkg-descr index 98e902c816b6..68abaf345515 100644 --- a/biology/seqan1/pkg-descr +++ b/biology/seqan1/pkg-descr @@ -6,5 +6,3 @@ This port includes only the library, the apps have been moved to biology/seqan-apps. This is the last release of the version 1 API, it is highly recommended to upgrade to biology/seqan (version 2). - -WWW: http://www.seqan.de/ diff --git a/biology/seqan3/pkg-descr b/biology/seqan3/pkg-descr index 8cb4595b3673..438e5e114acc 100644 --- a/biology/seqan3/pkg-descr +++ b/biology/seqan3/pkg-descr @@ -5,5 +5,3 @@ solutions by providing generic algorithms and data structures for: * full-text indexing and efficient search * sequence alignment * input/output of common file formats - -WWW: https://github.com/seqan/seqan3 diff --git a/biology/seqio/pkg-descr b/biology/seqio/pkg-descr index 3f71dc4f5497..8e0d717f3793 100644 --- a/biology/seqio/pkg-descr +++ b/biology/seqio/pkg-descr @@ -2,5 +2,3 @@ biological sequence files formatted using various file formats and which can be used to perform database searches on biological databases." - from the README file - -WWW: http://www.cs.ucdavis.edu/~gusfield/seqio.html diff --git a/biology/seqkit/pkg-descr b/biology/seqkit/pkg-descr index 3ea7639796e9..f1d66d437213 100644 --- a/biology/seqkit/pkg-descr +++ b/biology/seqkit/pkg-descr @@ -13,5 +13,3 @@ without any dependencies or pre-configurations. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. - -WWW: https://bioinf.shenwei.me/seqkit/ diff --git a/biology/seqtk/pkg-descr b/biology/seqtk/pkg-descr index 4cc42a9b9b87..d8d6aa596ef3 100644 --- a/biology/seqtk/pkg-descr +++ b/biology/seqtk/pkg-descr @@ -2,5 +2,3 @@ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. It performs basic file conversions and edits much like standard Unix tools do with text files. - -WWW: https://github.com/lh3/seqtk diff --git a/biology/sigviewer/pkg-descr b/biology/sigviewer/pkg-descr index bf5369429cc2..fbc66bd653c8 100644 --- a/biology/sigviewer/pkg-descr +++ b/biology/sigviewer/pkg-descr @@ -1,5 +1,3 @@ SigViewer is a viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information (such as annotations or artifact selections). - -WWW: https://github.com/cbrnr/sigviewer diff --git a/biology/slclust/pkg-descr b/biology/slclust/pkg-descr index c1ef243c32bb..85cfd2eb3d4d 100644 --- a/biology/slclust/pkg-descr +++ b/biology/slclust/pkg-descr @@ -1,5 +1,3 @@ Slclust is a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. - -WWW: https://sourceforge.net/projects/slclust/ diff --git a/biology/smithwaterman/pkg-descr b/biology/smithwaterman/pkg-descr index 8569aa85b397..75069997011d 100644 --- a/biology/smithwaterman/pkg-descr +++ b/biology/smithwaterman/pkg-descr @@ -4,5 +4,3 @@ protein sequences. Instead of looking at the entire sequence, the Smith-Waterman algorithm compares segments of all possible lengths and optimizes the similarity measure. Gotoh and Atschul added optimizations making it practical for larger problems. - -WWW: https://github.com/ekg/smithwaterman diff --git a/biology/snpeff/pkg-descr b/biology/snpeff/pkg-descr index cf47db97eb96..2d4fca4d95da 100644 --- a/biology/snpeff/pkg-descr +++ b/biology/snpeff/pkg-descr @@ -10,5 +10,3 @@ Features: GATK compatible (-o gatk) HGVS notation Sequence Ontology standardized terms - -WWW: http://snpeff.sourceforge.net/ diff --git a/biology/spoa/pkg-descr b/biology/spoa/pkg-descr index bbdf84e7cca3..3c926a5a84d7 100644 --- a/biology/spoa/pkg-descr +++ b/biology/spoa/pkg-descr @@ -5,5 +5,3 @@ generate consensus sequences. It supports three alignment modes: local and three gap modes: linear, affine and convex (piecewise affine). It also supports Intel SSE4.1+ and AVX2 vectorization (marginally faster due to high latency shifts), SIMDe and dispatching. - -WWW: https://github.com/rvaser/spoa diff --git a/biology/sra-tools/pkg-descr b/biology/sra-tools/pkg-descr index e9324dc5a96a..455877bb1565 100644 --- a/biology/sra-tools/pkg-descr +++ b/biology/sra-tools/pkg-descr @@ -14,5 +14,3 @@ from/to other formats that the 'next-gen' sequenecers generate including: The toolkit uses NCBI-VDB back-end enabling seamless access to remote SRA data and local SRA files. - -WWW: https://github.com/ncbi/sra-tools/wiki diff --git a/biology/stacks/pkg-descr b/biology/stacks/pkg-descr index f7c91c33e98f..91c14fbc8dfe 100644 --- a/biology/stacks/pkg-descr +++ b/biology/stacks/pkg-descr @@ -2,5 +2,3 @@ Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. - -WWW: http://catchenlab.life.illinois.edu/stacks/ diff --git a/biology/star/pkg-descr b/biology/star/pkg-descr index 28b0b0199bc9..61edfbda5a5a 100644 --- a/biology/star/pkg-descr +++ b/biology/star/pkg-descr @@ -7,5 +7,3 @@ by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 x 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision - -WWW: https://github.com/alexdobin/STAR diff --git a/biology/stringtie/pkg-descr b/biology/stringtie/pkg-descr index 246cda936a4b..923c100f4d95 100644 --- a/biology/stringtie/pkg-descr +++ b/biology/stringtie/pkg-descr @@ -7,5 +7,3 @@ Citation: Pertea et al. (2015) StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33: 290-295 doi:10.1038/nbt.3122 - -WWW: http://www.ccb.jhu.edu/software/stringtie/ diff --git a/biology/subread/pkg-descr b/biology/subread/pkg-descr index cb32c24836d6..8da3783515fc 100644 --- a/biology/subread/pkg-descr +++ b/biology/subread/pkg-descr @@ -16,5 +16,3 @@ next-gen sequencing read data including: exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises. - -WWW: http://bioinf.wehi.edu.au/subread-package/ diff --git a/biology/tRNAscan-SE/pkg-descr b/biology/tRNAscan-SE/pkg-descr index 4e6dafa3c065..1ed5b7acfb1d 100644 --- a/biology/tRNAscan-SE/pkg-descr +++ b/biology/tRNAscan-SE/pkg-descr @@ -6,5 +6,3 @@ strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats. - -WWW: http://lowelab.ucsc.edu/tRNAscan-SE/ diff --git a/biology/tabixpp/pkg-descr b/biology/tabixpp/pkg-descr index d92e83cdf94d..a1d8a78f73d3 100644 --- a/biology/tabixpp/pkg-descr +++ b/biology/tabixpp/pkg-descr @@ -1,5 +1,3 @@ This is a C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files. Tabix is a generic indexer for TAB-delimited genome position files. - -WWW: https://github.com/ekg/tabixpp diff --git a/biology/taxonkit/pkg-descr b/biology/taxonkit/pkg-descr index 4bec18ee74e9..5635706cc887 100644 --- a/biology/taxonkit/pkg-descr +++ b/biology/taxonkit/pkg-descr @@ -6,5 +6,3 @@ TaxonKit allows to: * filter TaxIds by taxonomic rank range * compute lowest common ancestor (LCA) for TaxIds * create TaxId changelog from dump archives - -WWW: https://bioinf.shenwei.me/taxonkit/ diff --git a/biology/treekin/pkg-descr b/biology/treekin/pkg-descr index dbe710e48068..7a7ed4e75806 100644 --- a/biology/treekin/pkg-descr +++ b/biology/treekin/pkg-descr @@ -1,5 +1,3 @@ treekin computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. - -WWW: https://www.tbi.univie.ac.at/RNA/Treekin/ diff --git a/biology/treepuzzle/pkg-descr b/biology/treepuzzle/pkg-descr index 1e51ea40d926..b13cc9d1a6af 100644 --- a/biology/treepuzzle/pkg-descr +++ b/biology/treepuzzle/pkg-descr @@ -14,5 +14,3 @@ TREE-PUZZLE are TN, HKY, F84, SH for nucleotides, Dayhoff, JTT, mtREV24, VT, WAG, BLOSUM 62 for amino acids, and F81 for two-state data. Rate heterogeneity is modeled by a discrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set. - -WWW: http://www.tree-puzzle.de diff --git a/biology/trimadap/pkg-descr b/biology/trimadap/pkg-descr index f872dd7b2215..bf1fb27adc00 100644 --- a/biology/trimadap/pkg-descr +++ b/biology/trimadap/pkg-descr @@ -4,5 +4,3 @@ adapter sequences with a few heuristic rules which can be found in the ta_trim1() function in trimadap-mt.c. The default adapters it uses are included in illumina.txt. These are typical Illumina adapters from paired-end sequencing. - -WWW: https://github.com/lh3/trimadap diff --git a/biology/trimmomatic/pkg-descr b/biology/trimmomatic/pkg-descr index 48c589bd5abd..acf81906fae5 100644 --- a/biology/trimmomatic/pkg-descr +++ b/biology/trimmomatic/pkg-descr @@ -1,4 +1,2 @@ Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. - -WWW: http://www.usadellab.org/cms/?page=trimmomatic diff --git a/biology/ucsc-userapps/pkg-descr b/biology/ucsc-userapps/pkg-descr index d2d01a997ea9..05129f558f62 100644 --- a/biology/ucsc-userapps/pkg-descr +++ b/biology/ucsc-userapps/pkg-descr @@ -4,5 +4,3 @@ tools. However, the license information at https://genome.ucsc.edu/license/ is not entirely clear and we may add non-free utilities in the future. Contact UCSC if you are using this port for commercial purposes. - -WWW: http://hgdownload.cse.ucsc.edu/admin/exe/ diff --git a/biology/ugene/pkg-descr b/biology/ugene/pkg-descr index 5e5f90fbac75..46c210fb96d9 100644 --- a/biology/ugene/pkg-descr +++ b/biology/ugene/pkg-descr @@ -8,5 +8,3 @@ retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees, and 3D structures. - -WWW: http://ugene.net/ diff --git a/biology/unikmer/pkg-descr b/biology/unikmer/pkg-descr index 7ae41bf53489..07f1ffcf165a 100644 --- a/biology/unikmer/pkg-descr +++ b/biology/unikmer/pkg-descr @@ -8,5 +8,3 @@ serialized in binary file with extension .unik. TaxIds can be assigned when counting k-mers from genome sequences, and LCA (Lowest Common Ancestor) is computed during set opertions including computing union, intersecton, set difference, unique and repeated k-mers. - -WWW: https://github.com/shenwei356/unikmer diff --git a/biology/vcf-split/pkg-descr b/biology/vcf-split/pkg-descr index 689705295fcb..37f7d39c7c92 100644 --- a/biology/vcf-split/pkg-descr +++ b/biology/vcf-split/pkg-descr @@ -4,5 +4,3 @@ with bcftools takes two days, so extracting the 137,977 samples one at a time or using thousands of parallel readers of the same file is impractical. Vcf-split solves this by generating thousands of single-sample outputs during a single sweep through the multi-sample input. - -WWW: https://github.com/auerlab/vcf-split diff --git a/biology/vcf2hap/pkg-descr b/biology/vcf2hap/pkg-descr index ef51e068d975..adf304a3605c 100644 --- a/biology/vcf2hap/pkg-descr +++ b/biology/vcf2hap/pkg-descr @@ -3,5 +3,3 @@ is required by haplohseq. vcf2hap is extremely fast and requires a trivial amount of memory regardless of the size of the VCF file. - -WWW: https://github.com/auerlab/vcf2hap diff --git a/biology/vcflib/pkg-descr b/biology/vcflib/pkg-descr index 977e86a03dae..8705b857d1d5 100644 --- a/biology/vcflib/pkg-descr +++ b/biology/vcflib/pkg-descr @@ -17,5 +17,3 @@ The API itself provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users. - -WWW: https://github.com/vcflib/vcflib diff --git a/biology/vcftools/pkg-descr b/biology/vcftools/pkg-descr index e9ceaa246e18..3bb9368e39a6 100644 --- a/biology/vcftools/pkg-descr +++ b/biology/vcftools/pkg-descr @@ -1,4 +1,2 @@ A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. - -WWW: https://github.com/vcftools/vcftools diff --git a/biology/velvet/pkg-descr b/biology/velvet/pkg-descr index da5c56fa485a..16bdb7b817ab 100644 --- a/biology/velvet/pkg-descr +++ b/biology/velvet/pkg-descr @@ -6,5 +6,3 @@ Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008) - -WWW: http://www.ebi.ac.uk/~zerbino/velvet/ diff --git a/biology/viennarna/pkg-descr b/biology/viennarna/pkg-descr index 6844f28badf9..dd5376f2a390 100644 --- a/biology/viennarna/pkg-descr +++ b/biology/viennarna/pkg-descr @@ -11,5 +11,3 @@ flexible structure and anchor constraints, and provides efficient computation of reliabilities in sequence-structure alignment. The package offers a robust core of features and is used as experimental platform for the incorporation of new features in RNA sequence-structure alignment. - -WWW: https://github.com/s-will/LocARNA diff --git a/biology/vsearch/pkg-descr b/biology/vsearch/pkg-descr index 86302327f8bf..f6c1015c060f 100644 --- a/biology/vsearch/pkg-descr +++ b/biology/vsearch/pkg-descr @@ -6,5 +6,3 @@ analysis, filtering, conversion and merging of paired-end reads. The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010). - -WWW: https://github.com/torognes/vsearch diff --git a/biology/vt/pkg-descr b/biology/vt/pkg-descr index 054cdd2824e9..14edbf90402a 100644 --- a/biology/vt/pkg-descr +++ b/biology/vt/pkg-descr @@ -1,4 +1,2 @@ vt is a variant tool set that discovers short variants from Next Generation Sequencing data. - -WWW: https://genome.sph.umich.edu/wiki/Vt diff --git a/biology/wise/pkg-descr b/biology/wise/pkg-descr index 6687f6352547..2dfc0a01a7f9 100644 --- a/biology/wise/pkg-descr +++ b/biology/wise/pkg-descr @@ -9,5 +9,3 @@ genewise, is one of the algorithms available in Wise2. There are other algorithms focused on EST data rather than genomic data, as well as some other algorithm curios." - from the web site (Ewan Birney) - -WWW: http://www.ebi.ac.uk/Wise2/ |