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quast

QUAST evaluates genome assemblies.

Versions:4.3
License:GPL2
Categories:bioinformatics assemblies
R

R environment for statistical computing and graphics

Versions:3.3.0
License:GPL, https://www.r-project.org/Licenses/
Categories:big data, data science, graphics, statistics
r-biomed-libs

R libraries for bioinformatics, genomics, and sequencing.

Versions:3.3
License:GPLv2
Categories:bioinformatics
raxml

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for post-analyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads.

Versions:8.2.8; 7.2.8
License:GNU GPL v3
Categories:Phylogentics, bioinformatics
repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns).

Versions:4.0.6
License:OSL-2.1
Categories:DNA sequence, DNA sequence masking., DNA sequence scanning
reportlab

The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics.

Versions:3.2.0
License:GPLv2
Categories:bioinformatics
Rgputools

R gputools library

Versions:R-3.3
License:GPL-3
Categories:CUDA, gpu, statistics
rmblast

RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite.

Versions:2.2.28
License:GPLv2
Categories:bioinformatics
Rmpi

R environment for statistical computing and graphics

Versions:3.3.0
License:GPL, https://www.r-project.org/Licenses/
Categories:big data, data science, graphics, statistics
roary

Roary is a high speed stand alone pan genome pipeline

Versions:3.7.0
License:GPLv3
Categories:bioinformatics
rsem

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.

Versions:1.2.31
License:GPLv3
Categories:bioinformatics
RStudio-server

RStudio Server IDE is a powerful and productive user interface for R. This is a special version of RStudio Server used by ARC Connect ( https://connect.arc-ts.umich.edu/ )

Versions:0.99.903
License:AGPL
Categories:ARC Connect, IDE, big data, data science, graphics, statistics, web
sage

SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.

Versions:7.2
License:GNU GPL v3
Categories:Math, Programming
samtools

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.

Versions:0.1.19; 1.2; 1.3.1
License:GPLv3
Categories:bioinformatics
sas

SAS statistical system software.

Versions:9.4
License:Not available
Categories:Statitics, econometrics
scipy-dev

Scientific libraries for use within Python.

Versions:0.17.1
License:http://www.scipy.org/scipylib/license.html
Categories:Programming, python, solver
sickle

A windowed adaptive trimming tool for FASTQ files using quality

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

SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.

Versions:3.9.0
License:GNU GPL v2
Categories:Assembly, 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
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:2.7.0
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:1.41; 1.35
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
License:http://www.stata.com/order/end-user-license-agreement/
Categories:econometrics, statistics
stata-mp

Statistical analysis software.

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

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

Versions: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
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:
tophat

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

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

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

Versions:160726
License:https://raw.githubusercontent.com/torch/torch7/master/COPYRIGHT.txt
Categories:CUDA, machine learning
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
License:https://raw.githubusercontent.com/trinityrnaseq/trinityrnaseq/master/LICENSE
Categories:Assembly, Transcriptome, bioinformatics
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Total pages: 7
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