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stacks

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.

Versions:1.35; 1.41; 1.45
License:GNU GPL v3
Categories:Genomics, Pipeline, phylogenetics
star

Spliced Transcripts Alignment to a Reference

Versions:2.5.2a
License:GPLv3
Categories:bioinformatics
starccm

Star-CCM+ is a CFD application that supports parallel processing.

Versions:11.04.010; 11.04.010-R8
License:CFD
Categories:
stata

Statistical analysis software.

Versions:14; 15
License:http://www.stata.com/order/end-user-license-agreement/
Categories:econometrics, statistics
stata-mp

Statistical analysis software.

Versions:14; 15
License:http://www.stata.com/order/end-user-license-agreement/
Categories:econometrics, statistics
strelka

Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples.

Versions:1.0.15
License:GPLv3
Categories:bioinformatics
stringtie

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

Versions:1.3.3b; 1.2.4
License:Artistic 2.0
Categories:bioinformatics
subread

a tool kit for processing next-gen sequencing data

Versions:1.5.0
License:GPLv2
Categories:bioinformatics
swig

SWIG is an interface compiler.

Versions:3.0.10
License:http://www.swig.org/legal.html
Categories:Compiler, Programming
szip

Szip is a compression library used with HDF5.

Versions:2.1
License:https://www.hdfgroup.org/doc_resource/SZIP/
Categories:Utility, compression
tabix

A useful tool that indexes large .vcf files

Versions:0.2.6
License:GPLv2
Categories:bioinformatics
taco

Multi-sample transcriptome assembly from RNA-Seq

Versions:0.5.1
License:http://tacorna.github.io/#license
Categories:Application, Biostatistics, python
tax2tree

The tax2tree software package was developed in collaboration with Greengenes for the purpose of transferring a taxonomy from one tree to another. Specifically, the motivation was to reduce the manual curation effort necessary for each release of Greengenes by automating the decoration of taxonomy.

Versions:1.0
License:Unknown
Categories:
tecplot

Plotting and visualization software that gives full control over 2-D and 3-D plot parameters.

Versions:2016
License:plotting, visualization
Categories:
thermocalc

software package for thermodynamic calculations

Versions:2016a
License:Academic Research license
Categories:thermodynamic
tophat

TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions.

Versions:2.0.11; 2.0.0
License:GPLv3
Categories:bioinformatics
torch

Torch is a scientific computing framework with wide support for machine learning algorithms.

Versions:170802; 160726
License:https://raw.githubusercontent.com/torch/torch7/master/COPYRIGHT.txt
Categories:CUDA, machine learning
transdecoder

TransDecoder identifies candidate coding regions within transcriptsequences, such as those generated by de novo RNA-Seq transcript assemblyusing Trinity, or constructed based on RNA-Seq alignments to the genomeusing Tophat and Cufflinks.

Versions:5.0.1
License:BSD 3-clause
Categories:bioinformatics sequencing coding transcript
trilinos

Trilinos is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.

Versions:12.8.1
License:https://trilinos.org/download/license/
Categories:engineering, multi-physics
trimgalore

Consistent quality and adapter trimming for RRBS or standard FastQ files

Versions:0.4.2
License:https://www.gnu.org/licenses/gpl-3.0.en.html
Categories:Perl, Script, bioinformatics
trimmomatic

Trimmomatic: A flexible read trimming tool for Illumina NGS data

Versions:0.36
License:GNU GPL v3
Categories:Sequencing, bioinformatics
trinity

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Versions:2.2.0; 2.4.0; 2.3.2
License:GPLv2
Categories:bioinformatics
uclust

UCLUST v1.2.22q (C) Copyright 2009-10 Robert C. Edgar.

Versions:1.2.22q
License:These binaries are licensed only for use in PyNAST and QIIME. The license does not permit stand-alone use.
Categories:
udunits

The UDUNITS-2 package provides support for units of physical quantities.

Versions:2.2.20
Categories:Conversion, Units
unanimity

C++ library and its applications to generate and process accurate consensus sequences

Versions:2.1.0; 2.0.4
License:GPLv2
Categories:bioinformatics
usearch

USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

Versions:8.1
License:GPLv3
Categories:bioinformatics
valet

This software is Open Source. almaBTE is a pipeline for detecting mis-assemblies in metagenomic assemblies.

Versions:1.0
License:https://github.com/marbl/VALET
Categories:Genomics
valgrind

Valgrind is an instrumentation framework for building dynamic analysis tools.

Versions:3.11.0
License:GNU GPL v2
Categories:Instrumentation, Utilities
vasp

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] VASP, The Vienna Ab initio simulation package, a plane wave electronic structure code.

Versions:old-5.3.5.31Mar2014; 5.4.4.18Apr17; 5.4.1.05Feb16.p2.b; old-5.3.3.18Dec2012; old-5.3.5.31Mar2014wannier90v12; old-4.6.36Feb09; old-5.2.12.11Nov2011; 5.4.1.05Feb16.p2; old-5.3.2.13Sep2012
License:https://www.vasp.at/index.php/faqs
Categories:electronic structure code, molecular dynamics
vcfanno

Vcfanno provides fast, flexible annotation of genetic variants

Versions:0.1.1-rc2
License:GPLv3
Categories:bioinformatics
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
Current page: 9
Total pages: 10
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