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sift4g

SIFT 4G takes a query sequence and uses multiple alignment information to predict tolerated and deleterious substitutions for every position of the query sequence.

Versions:2.0.0
License:GPLv2
Categories:bioinformatics
slepc

SLEPc, the Scalable Library for Eigenvalue Problem Computations. The library is used to compute eigenvalues and eigenvectors of large, sparse matrices with iterative methods.

Versions:3.7.4
License:GNU LGPL license
Categories:eigenvalues, eigenvectors
smrtanalysis

A software suite designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.

Versions:2.3.0
License:GPLv2
Categories:bioinformatics
SNAP

SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser.

Versions:2013-11-29
License:MIT (https://opensource.org/licenses/MIT)
Categories:Gene finding, HMM, eukaryotic genome, prokaryotic genome
sonnet

[SPECIAL LICENSE REQUIRED: contact hpc-support@umich.edu] EnSight is a post processing and visualization tool.

Versions:16.0
License:https://www.sonnetsoftware.com/products/lite/license.html
Categories:design, simulation
spades

SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines

Versions:3.9.0; 3.10.0
License:GPLv3
Categories:bioinformatics
sparsehash

The Google SparseHash project contains several hash-map implementations in use at Google, with different performance characteristics, including an implementation that optimizes for space and one that optimizes for speed.

Versions:2.0.3
License:https://raw.githubusercontent.com/sparsehash/sparsehash/master/COPYING
Categories:Programming, library
spglib

Spglib is a library for finding and handling crystal symmetries written in C.

Versions:1.9.8
License:New BSD
Categories:crystal symmetries, k-points
spparks

sppakrs is a Monte Carlo program.

Versions:18May17
License:http://spparks.sandia.gov/open_source.html
Categories:Monte Carlo, crystal symmetries
sratoolkit

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

Versions:2.8.2-1; 2.7.0
License:GPLv2
Categories:bioinformatics
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:12.00.000-R8; 11.04.010; 11.04.010-R8; 12.04.010-R8; 12.04.010
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:2.0.9; 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
Current page: 9
Total pages: 10
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