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scythe

Scythe is a Bayesian adapter trimmer .

Versions:0.993
License:https://github.com/vsbuffalo/scythe
Categories:Genomics, Sequencing, gene, omics
selectionStats

This script calculates diversity and selection statistics for fasta alignments.

Versions:1.0
License:MIT
Categories:bioinformatics
seqmule

Automated human exome/genome variants detection

Versions:1.2.6
License:GPLv2
Categories:bioinformatics
SETSM

SETSM: fully automatic algorithm for deriving Digital Terrain Models (DTM) from pairs of satellite imagery

Versions:3.3.1 with intel/3.3.1
License:Apache 2.0
Categories:Mapping
sga

SGA – String Graph Assembler

Versions:0.10.15
License:GPL
Categories:Genomics
sicer

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

Versions:1.1
License:GPLv2
Categories:bioinformatics
sickle

A windowed adaptive trimming tool for FASTQ files using quality

Versions:1.33.6
License:MIT software license
Categories:bioinformatics trimming fastq
siesta

SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

Versions:4.1-b3
License:Electronic Structure, ab initio, quantum, dft
Categories:
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:3.8.3; 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
soapdenovo2

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.

Versions:2.04-r241
License:GPL
Categories:Genomics
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
stampy

a swiss-army knife of tools for a wide-range of genomics analysis tasks.

Versions:1.0.32
License:GPLv2
Categories:bioinformatics
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:1.6.1; 1.5.0
License:GPLv2
Categories:bioinformatics
subversion

Apache Subversion centralized version control system.

Versions:1.10.0-1
License:https://www.apache.org/licenses/LICENSE-2.0
Categories:SVN, reversion control, version control
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; 12.8.1-gcc-5.4.0-openmpi-3.0.0; 12.12.1-gcc-5.4.0-openmpi-1.10.2; .12.8.1 with openmpi/3.0.0 gcc/5.4.0
License:https://trilinos.org/download/license/
Categories:engineering, multi-physics
Current page: 10
Total pages: 11
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