List of Supported Software

casacore

A suite of C++ libraries for radio astronomy data processing.

https://casacore.github.io

Zeus

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Galaxy

CFITSIO is a library of ANSI C routines for reading and writing FITS format data files.

https://heasarc.gsfc.nasa.gov/fitsio/fitsio.html

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Galaxy

Ansys publishes engineering analysis software across a range of disciplines including finite element analysis, structural analysis, computational fluid dynamics, explicit and implicit methods, and heat transfer.

http://www.ansys.com

Zeus

Fluent

ANSYS Fluent is the most-powerful computational fluid dynamics (CFD) software tool available, empowering you to go further and faster as you optimize your products performance. Fluent includes well-validated physical modelling capabilities to deliver fast, accurate results across the widest range of CFD and multiphysics applications.

(Please read: Ansys Licensing )

http://www.ansys.com/Products/Fluids/ANSYS-Fluent

Zeus

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CFX

ANSYS CFX is a high-performance computational fluid dynamics (CFD) software tool that delivers reliable and accurate solutions quickly and robustly across a wide range of CFD and multi-physics applications.

(Please read: Ansys Licensing )

http://www.ansys.com/Products/Fluids/ANSYS-CFX

Zeus

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OpenFOAM

OpenFOAM is an open-source CFD package, providing solvers, visualisation tools, and pre- and post-processing utilities. This module provides the OpenFOAM foundation version of OpenFOAM.

http://openfoam.org

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OpenFOAM is an open-source CFD package, providing solvers, visualisation tools, and pre- and post-processing utilities. This module provides the ESI version of OpenFOAM.

http://openfoam.com

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ALLPATHS-LG is a whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. The significant difference between ALLPATHS and
traditional assemblers such as Arachne is that ALLPATHS assemblies are not necessarily linear, but instead are presented in the form of a graph. This graph representation retains ambiguities, such as those arising from polymorphism, uncorrected read errors, and unresolved repeats, thereby providing information that has been absent from previous genome assemblies.

http://software.broadinstitute.org/allpaths-lg/blog/

The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler. Open-source so that everyone is welcome to contribute and help build outstanding assembly tools, and modular in nature so that new contributions can be easily inserted into an existing assembly pipeline. This modular design will foster the development of new assembly algorithms and allow the AMOS project to continually grow and improve in hopes of eventually becoming a widely accepted and deployed assembly infrastructure. In this sense, AMOS is both a design philosophy and a software system.

http://amos.sourceforge.net/wiki/index.php/AMOS

AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on a web server or be downloaded and run locally. It is open source.

http://bioinf.uni-greifswald.de/augustus/

Tools for common BAM file manipulations.

https://github.com/hall-lab/bamkit

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

https://samtools.github.io/bcftools/bcftools.html

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BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.

http://ant.apache.org://github.com/beagle-dev/beagle-lib

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BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

https://www.beast2.org/

Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools lets you intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

http://bedtools.readthedocs.io/en/latest/

Bioperl is an open source bioinformatics toolkit used by researchers all over the world. If youre looking for a script built to fit your exact needs you may or may not find it in Bioperl (check the scripts and examples directories). What you will find is an extensive set of Perl modules that will enable you to write your own script, and a community of people who are willing to help you.

http://bioperl.org/

Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. The source code is made available under the Biopython License, which is extremely liberal and compatible with almost every license in the world.

http://biopython.org/

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Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.

https://www.bioinformatics.babraham.ac.uk/projects/bismark/

BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.

https://blast.ncbi.nlm.nih.gov/

BLAST+ is a suite of command-line tools to run BLAST. For details, please see the BLAST+ user manual, the BLAST Help manual, the BLAST releases notes, and the article in BMC Bioinformatics. BLAST+ is the most current version of BLAST and is the only supported version.

https://blast.ncbi.nlm.nih.gov/

Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome. By default, the index consists of all non-overlapping 11-mers except for those heavily involved in repeats, and it uses less than a gigabyte of RAM. This smaller size means that Blat is far more easily mirrored than BLAST. Blat of DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments.

https://genome.ucsc.edu/cgi-bin/hgBlat

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small.

http://bowtie-bio.sourceforge.net/index.shtml

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB.

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

BreakDancer-1.1, released under GPLv3, is a Perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation.

http://breakdancer.sourceforge.net/

BSMAP is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.

https://code.google.com/archive/p/bsmap/

BS Seeker 2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated short reads.

http://pellegrini.mcdb.ucla.edu/BS_Seeker2/

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BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.

http://bio-bwa.sourceforge.net/

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Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).

http://canu.readthedocs.io/

Cap3 is an assembly program. It is used to assemble sequences into contigs. On Bio-Linux, it is required by the ESTFerret program.

http://seq.cs.iastate.edu/cap3.html

CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset.

http://weizhongli-lab.org/cd-hit/

ChunkChromosome is a helper utility for minimac and MaCH. It can be used to facilitate analyses of very large datasets in overlapping slices.

https://genome.sph.umich.edu/wiki/ChunkChromosome

Clustal W is a general purpose multiple alignment program for DNA or proteins.

http://www.clustal.org/clustal2/

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Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

http://cole-trapnell-lab.github.io/cufflinks/

EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

http://emboss.sourceforge.net/

Eval is a flexible tool for analyzing the performance of gene-structure prediction programs. It provides summaries and graphical distributions for many statistics describing any set of annotations, regardless of their source. It also compares sets of predictions to standard annotations and to one another.

http://mblab.wustl.edu/software.html

ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters.

https://sco.h-its.org/exelixis/web/software/exabayes/index.html

Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.

http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

The FastML server is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences.

http://fastml.tau.ac.il/

A quality control tool for high throughput sequence data.

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. Here, we summarize how to setup this software package, compile the C and Cython scripts and run the algorithm on a test simulated genotype dataset.

https://rajanil.github.io/fastStructure/

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The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.

http://hannonlab.cshl.edu/fastx_toolkit/

FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

https://github.com/ekg/freebayes

Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis.

GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.

http://cnsgenomics.com/software/gcta/

geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, start and stop codons are predicted and scored along the sequence using Position Weight Arrays (PWAs). In the second step, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the the log-likelihood ratio of a Markov Model for coding DNA. Finally, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons.

http://genome.crg.es/software/geneid/

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach is described in our original Nucleic Acids Research paper on Glimmer 1.0 and in our subsequent paper on Glimmer 2.0. The IMM is a combination of Markov models from 1st through 8th-order, where the order used is determined by the amount of data available to train the model. In addition, the positions used as context for the model need not immediately precede the predicted postion but are determined by a decision procedure based on the predictive power of each position in the training data set (which we term an Interpolated Context Model or ICM). The models for coding sequence are 3-periodic nonhomogenous Markov models. Improvements made in version 3 of Glimmer are described in the third Glimmer paper.

http://ccb.jhu.edu/software/glimmer/

GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilises Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).

http://ccb.jhu.edu/software/glimmerhmm/

GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.

http://research-pub.gene.com/gmap/

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

http://hmmer.org/

HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.

https://github.com/samtools/htslib

InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.

http://www.ebi.ac.uk/interpro/interproscan.html

Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the compare-and-swap CPU instruction to increase parallelism.

http://www.genome.umd.edu/jellyfish.html

The khmer software is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data.

https://github.com/dib-lab/khmer

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LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

http://www.bx.psu.edu/~rsharris/lastz/

Gordon's Text utils Library.

https://github.com/agordon/libgtextutils

ChunkChromosome is a helper utility for minimac and MaCH. It can be used to facilitate analyses of very large datasets in overlapping slices.

https://genome.sph.umich.edu/wiki/ChunkChromosome

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~30,000 sequences), etc.

http://mafft.cbrc.jp/alignment/software/

The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.

https://micans.org/mcl/

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.

http://mrbayes.sourceforge.net/

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MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

http://mummer.sourceforge.net/

MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes - only a handful of command-line options are needed to perform common alignment tasks.

http://www.drive5.com/muscle/

NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end engines. The engine for accessing SRA data is contained within the sister repository ncbi-vdb.

https://github.com/ncbi/ngs

De novo transcriptome assembler for very short reads.

https://www.ebi.ac.uk/~zerbino/oases/

PLINK is a whole genome association analysis toolset, designed to perform a range fo basic, large-scale analyses in a computationally efficient manner.

http://zzz.bwh.harvard.edu/plink/

PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.

Tool for genome-wide association analysis of imputed genetic data.

The benefit of pyRAD over most alternative methods for analyzing RADseq-like data comes in its use of an alignment-clustering method (vsearch) that allows for the inclusion of indel variation which improves identification of homology across highly divergent samples. For this reason pyRAD is commonly employed for RADseq studies at deeper phylogenetic scales, however, it works equally well at shallow scales.

http://dereneaton.com/software/pyrad/

Pysam is a python module for reading, manipulating and writing genomic data sets. Pysam is a wrapper of the htslib C-API and provides facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing.

https://pysam.readthedocs.io/en/latest/

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A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.

https://sco.h-its.org/exelixis/web/software/raxml/index.html

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualisation, it can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.

https://deweylab.github.io/RSEM/

samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file.

https://github.com/GregoryFaust/samblaster

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

http://samtools.sourceforge.net/

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Scarpa is a stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data. Scarpa is available free of charge for academic and commercial use under the GNU General Public License (GPL).

http://compbio.cs.toronto.edu/hapsembler/scarpa.html

Screed is a biological sequence parsing and storage/retrieval library for DNA and protein sequences.

https://pypi.python.org/pypi/screed

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Slightly hacked version of Heng Li's seqtk for fastq-to-fasta conversions for Trinity compatibility.

https://github.com/trinityrnaseq/seqtk-trinity

SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.

https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html

Windowed Adaptive Trimming for fastq files using quality.

https://github.com/najoshi/sickle

Implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences.

https://github.com/relipmoc/skewer

SNAP is a new sequence aligner that is 3-20x faster and just as accurate as existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools (in some cases) and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.

http://snap.cs.berkeley.edu/

Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).

http://snpeff.sourceforge.net/

A quality control tool for high throughput sequence data.

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

SOAP3 is a GPU-based software for aligning short reads to a reference sequence. It can find all alignments with k mismatches, where k is chosen from 0 to 4. When compared with its previous version SOAP2, SOAP3 can be up to tens of times faster. For example, when aligning length-100 reads with the human genome, SOAP3 is the first software that can find all 4-mismatch alignments in tens of seconds per million reads.

http://i.cs.hku.hk/2bwt-tools/soap3/index.html

SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. Now the new version is available. SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.

http://soap.genomics.org.cn/soapdenovo.html

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

http://cab.spbu.ru/software/spades/

Sequence Read Archive (SRA) makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries by comparing data sets. The SRA stores raw sequencing data and alignment information from high-throughput sequencing platforms.

https://www.ncbi.nlm.nih.gov/sra

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.

http://catchenlab.life.illinois.edu/stacks/

Spliced Transcripts Alignment to a Reference.

https://github.com/alexdobin/STAR

The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.

http://web.stanford.edu/group/pritchardlab/structure.html

Bayesian genotyper for structural variants.

https://github.com/hall-lab/svtyper

TASSEL project is a Java platform designed for the optimized analysis of crop
genomic diversity.

https://bitbucket.org/tasseladmin/tassel-5-standalone

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

https://ccb.jhu.edu/software/tophat/index.shtml

Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. There is no need to specify the pattern, the size of the pattern or any other parameter.

https://tandem.bu.edu/trf/trf.html

Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. There is no need to specify the pattern, the size of the pattern or any other parameter.

https://tandem.bu.edu/trf/trf.html

Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.

http://www.usadellab.org/cms/?page=trimmomatic

Trinity, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

https://github.com/trinityrnaseq/trinityrnaseq/wiki

tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second. It was implemented for large-scale human genome sequence analysis, but is applicable to other DNAs as well.

http://eddylab.org/software.html

UCSC Tools.

http://hgdownload.soe.ucsc.edu

An awk-like VCF parser.

https://github.com/cc2qe/vawk

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.

https://vcftools.github.io/index.html

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.

VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, 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, conversion and merging of paired-end reads.

https://github.com/torognes/vsearch

Celera Assembler : scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing.

http://wgs-assembler.sourceforge.net/

The Wise2 package is now a rather stately bioinformatics package that has be around for a while. Its key programs are 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.

http://www.ebi.ac.uk/~birney/wise2/

Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

http://ambermd.org/

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The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.

http://www.cpmd.org/

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

http://www.gromacs.org/

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LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems.

https://lammps.sandia.gov

Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems, along with our MPB eigenmode package.

http://ab-initio.mit.edu/wiki/index.php/Meep

The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics framework primarily developed by Idaho National Laboratory. It provides a high-level interface to some of the most sophisticated nonlinear solver technology on the planet. MOOSE presents a straightforward API that aligns well with the real-world problems scientists and engineers need to tackle.

http://mooseframework.org

NAMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code.

http://www.ks.uiuc.edu/Research/namd/

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NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

http://www.nwchem-sw.org/index.php/Main_Page

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PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short range repulsive interactions do not disrupt the simulations.

http://www.ime.unicamp.br/~martinez/packmol/home.shtml

PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.

http://www.plumed.org

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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. SIESTAs efficiency stems from the use of strictly localized basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. A very important feature of the code is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods.

https://departments.icmab.es/leem/siesta/

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases.

http://towhee.sourceforge.net

The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

https://www.vasp.at/

ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques.

https://www.paraview.org/

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. From Unix, Windows or Mac workstations, users can interactively visualize and analyze data ranging in scale from small (<101 core) desktop-sized projects to large (>105 core) leadership-class computing facility simulation campaigns.

https://wci.llnl.gov/simulation/computer-codes/visit

The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing, and visualization. It
consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including scalar, vector, tensor, texture, and volumetric methods, as well as advanced modeling techniques such as implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.

http://www.vtk.org/

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

http://www.ks.uiuc.edu/Research/vmd/

OpenCV (Open Source Computer Vision Library) is released under a BSD license and hence it’s free for both academic and commercial use. It has C++, Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware acceleration of the underlying heterogeneous compute platform.

https://opencv.org

NCL is an interpreted language designed specifically for scientific data analysis and visualisation.

https://www.ncl.ucar.edu/

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

https://www.r-project.org/about.html

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proj.4 is a standard UNIX filter function which converts geographic longitude and latitude coordinates into cartesian coordinates (and vice versa), and it is a C API for software developers to include coordinate transformation in their own software.

http://proj4.org/

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Singularity enables container images for HPC, allowing end-users to safely and efficiently run a Docker image on a HPC system.

https://sylabs.io/singularity/

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gnuplot

Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. The source code is copyrighted but freely distributed (i.e., you don't have to pay for it). It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave.

http://www.gnuplot.info

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FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created. It supports the most obscure ancient formats up to the cutting edge. No matter if they were designed by some standards committee, the community or a corporation. It is also highly portable: FFmpeg compiles, runs, and passes our testing infrastructure FATE across Linux, Mac OS X, Microsoft Windows, the BSDs, Solaris, etc. under a wide variety of build environments, machine architectures, and configurations.

https://ffmpeg.org/

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libctl is a free Guile-based library implementing flexible control files for scientific simulations. It was written to support our MIT Photonic Bands and Meep software, but has proven useful in other programs too.

http://ab-initio.mit.edu/wiki/index.php/Libctl

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The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.

https://sourceware.org/libffi/

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Fast Light Toolkit. FLTK (pronounced fulltick) is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and macOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.

http://www.fltk.org/

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