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vcftools

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

Versions:0.1.14
License:GPLv3
Categories:
velvet

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies such as Solexa or 454.

Versions:1.2.10; 1.2.10-big
License:GNU GPL v2
Categories:Assembly, bioinformatics
vep

The Variant Effect Predictor predicts the functional effects of genomic variants

Versions:89.7
License:GPLv2
Categories:bioinformatics
virsorter

VirSorter: mining viral signal from microbial genomic data

Versions:1.0.3
License:GPL2
Categories:bioinformatics genomic virus microbe
vsearch

We have implemented a tool called VSEARCH which supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion.

Versions:2.0.2
License:GNU GPL v3 or under the BSD 2-clause license
Categories:Metagenomics, bioinformatics
vt

a variant tool set that discovers short variants from Next Generation Sequencing data

Versions:0.57
License:GPLv2
Categories:bioinformatics
wannier90

Maximally-localised Wannier functions (MLWFs) and Wannier90

Versions:2.0.0; 2.0.1; 1.2
License:http://www.wannier.org
Categories:MLWFs, electronic structure code
wcstools

WCSTools is a package of programs and a library of utility subroutines for setting and using the world coordinate systems (WCS) in the headers of the most common astronomical image formats, FITS and IRAF .imh, to relate image pixels to sky coordinates.

Versions:3.9.3
License:GNU GPL
Categories:FITS, IRAF, WCS, Woorld Coordinate System
weblogo

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.

Versions:2.8.2
License:GPLv2
Categories:bioinformatics
wgs-assembler

Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.

Versions:8.3
License:GNU GPL v2
Categories:Celera, Sequencing, bioinformatics
wigToBigWig

The wigToBigWig program converts a ‘wig’ file to ‘bigWig’ format.

Versions:4.0.0
License:GPLv3
Categories:bioinformatics
wise2

Wise2 includes genewise, a program for aligning proteins or protein HMMs to DNA, and dynamite a rather cranky “macro language”” which automates the production of dynamic programming. “

Versions:2.4.1
License:GNU GPL
Categories:bioinformatics
wrf

The Weather Research and Forecasting (WRF) Model is atmospheric modeling system designed for both meteorological research and numerical weather prediction.

Versions:3.8
License:http://www2.mmm.ucar.edu/wrf/users/public.html
Categories:Weather Forecasting, atmospheric modeling, meteorology
xcrysden

XCrySDen is a molecular/crystal structure visualization program.

Versions:1.5.60
License:http://www.xcrysden.org/License.html
Categories:crystal symmetries, electronic structure, vizualization
yasm

Yasm assembler.

Versions:1.3.0
License:https://github.com/yasm/yasm/blob/master/BSD.txt
Categories:Programming, assembler
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