Software

Software supported by NCGAS

The National Center for Genome Analysis Support (NCGAS) and its collaborators maintain the following genome analysis packages on Carbonate and Karst at Indiana University, on Bridges at Pittsburgh Supercomputing Center (PSC), and via images on Jetstream. For more information on a package, click its name. If the package you need is not listed in the table below, contact NCGAS.

Package	Description	Version	Carbonate	Karst	Bridges	Jetstream
abyss	Parallel assembler for short read sequence data	1.5.2	✔Yes		✔Yes	Genomics Toolkit
		1.9.0			✔Yes
		2.0.2	✔Yes		✔Yes
admixture	A tool to estimate individual ancestry from single nucletotide polymorphism (SNP) data sets.	1.3.0		✔Yes
admixture		5.1		✔Yes
AllPaths-LG	Whole-genome shotgun assembler using Illumina long and short read library	524888			✔Yes
Annovar	Functionally annotates genetic variants detected from diverse genomes	2016.02.01			✔Yes
AFNI	Processing, analyzing, and displaying functional MRI (FMRI) data	1 .0.13	✔Yes
		1 .3.03	✔Yes
		16.3.00		✔Yes
Anvi'o	Analysis and visualization of genomics data	2.0.2			✔Yes	Anvio Mining SRA to identify datasets
		2.2.2			✔Yes
		2.3.1			✔Yes
		2.3.2			✔Yes
		2.4.0			✔Yes
		3.0.0			✔Yes
ARAGORN	Detects tRNA, mtRNA and tmRNA genes	1.2.3			✔Yes
augustus	Predicts genes in eukaryotic genomic sequences	3.3	✔Yes	✔Yes		Genome assembly workshop
augustus	Predicts genes in eukaryotic genomic sequences	3.2			✔Yes
autodocksuite	Predicts how small molecules, e.g., substrates or drug candidates, bind to a receptor of known 3D structure	4.2.3		✔Yes
autodocksuite		4.2.6			✔Yes
bamtools	C++ API and toolkit for analyzing and managing BAM files	2.4.0			✔Yes	bcbio-nextgen toolkit v.2.0 Genomics Toolkit Genome assembly workshop
bamtools	C++ API and toolkit for analyzing and managing BAM files	2.4.1	✔Yes	✔Yes
bamutil	Several programs that perform operations on SAM/BAM files	1.0.13		✔Yes		bcbio-nextgen toolkit v.2.0
bamutil	Several programs that perform operations on SAM/BAM files	1.0.14	✔Yes
Barrnap	Predicts location of ribosomal RNA genes in genomes	0.6			✔Yes
bbmap	Short read aligner for DNA and RNA-seq data	38.6				Genomics Toolkit
bcftools	Discovery of correlated genomic features, such as ESTs, polymorphisms, and mobile elements	1.3.1		✔Yes	✔Yes	Genomics Toolkit
		0.1.19			✔Yes
		1.5	✔Yes
Bedops	Scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale	2.4.19			✔Yes
Bedops		2.4.35			✔Yes
BLASR	Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement	1.3.1	✔Yes		✔Yes
bedtools	Discovery of correlated genomic features, such as ESTs, polymorphisms, and mobile elements	2.20.1		✔Yes		bcbio-nextgen toolkit v.2.0 Genomics Toolkit
		2.26.0	✔Yes	✔Yes
		2.25.0			✔Yes
bfast	Blat-like Fast Accurate Search Tool (BFAST) facilitates the fast and accurate mapping of short reads to reference sequences	0.7.0a		✔Yes
bioconductor	R packages for analysis and comprehension of high-throughput genomic sequence data	2.12		✔Yes		R for Biologists Harvesting Field Station Data
		3.1		✔Yes
		3.3	✔Yes	✔Yes
		3.6	✔Yes
		3.9	✔Yes	✔Yes
biopython	Collection of python packages to support bioinformatics	1.59		✔Yes		bcbio-nextgen toolkit v.2.0
		1.7.0	✔Yes	✔Yes
		1.7.3	✔Yes
Bismark	Program to map bisulfite treated sequencing reads to a genome of interest	0.19.0	✔Yes		✔Yes
blast	Search tool that finds regions of local similarity between nucleotide or protein sequences	2.6.0+	✔Yes		✔Yes	Genomics Toolkit Genome assembly workshop
		2.2.27		✔Yes
		2.2.2		✔Yes
		2.2.31		✔Yes	✔Yes
		2.7.1			✔Yes
blat	Alignment tool like BLAST, but structured differently	35	✔Yes	✔Yes	✔Yes
bowtie	Ultrafast, memory-efficient short read aligner. See related tool Bowtie2.	1.1.2		✔Yes	✔Yes	bcbio-nextgen toolkit v.2.0 Genomics Toolkit
		1.1.1			✔Yes
		1.2.2	✔Yes
bowtie2	Ultrafast, memory-efficient tool for aligning sequencing reads to long reference sequences. See related tool Bowtie.	2.1.0		✔Yes		bcbio-nextgen toolkit v.2.0 Arkansas Workshop Genomics Toolkit
		2.2.3		✔Yes
		2.2.6		✔Yes
		2.2.7			✔Yes
		2.3.2	✔Yes
		2.3.4.1			✔Yes
		2.3.5		✔Yes
busco	Assesses genome assembly and annotation completeness	3.0.2	✔Yes			Arkansas Workshop Genome assembly workshop
busco	Assesses genome assembly and annotation completeness	1.22			✔Yes
breakdancer	Provides genome-wide detection of structural variants from next generation paired-end sequencing reads	1.1		✔Yes
breakdancer		1.3.6		✔Yes
breseq	Finds mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes	0.23		✔Yes
		0.30.0		✔Yes
		0.30.2	✔Yes
		0.32.0	✔Yes
bwa	Fast light-weight tool that aligns relatively short sequences to a sequence database	0.6.2				bcbio-nextgen toolkit v.2.0 Genomics Toolkit
		0.7.10		✔Yes
		0.7.12	✔Yes
		0.7.15		✔Yes
cafe	Analyze changes in gene family size for evolutionary inferences	4.2	✔Yes
canu	Fork of the Celera Assembler designed for high-noise single-molecule sequencing	1.3		✔Yes	✔Yes
		1.4		✔Yes
		1.5			✔Yes
		1.6	✔Yes		✔Yes
		1	✔Yes
		1.7		✔Yes
cd-hit	Tool to cluster and compare protein or nucleotide sequences	4.6.	✔Yes
cd-hit	Tool to cluster and compare protein or nucleotide sequences	2016.06.21			✔Yes
centrifuge	Rapid and efficient classification of DNA sequences from microbial samples	1.0.3	✔Yes		✔Yes
centrifuge		1.0.4			✔Yes
cfsan	Python based SNP pipelines	1.0.1	✔Yes
checkm	Tools for assessing genome quality recovered from isolates, single cells or metagenomes	1.0.7			✔Yes	Arkansas Workshop
Circos	Produces visualizations in a circular layout, commonly used for genomics data	0.69.2			✔Yes
clustalw2	Multiple alignment of nucleic acid and protein sequences	2.0.12		✔Yes
clustalw2	Multiple alignment of nucleic acid and protein sequences	2.1			✔Yes
colormap	ColorMap is a hybrid method for correcting noisy long reads	1		✔Yes
crisprdo	Evaluate the goodness of an sgRNA in both sensitivity and specificity	1		✔Yes		bcbio-nextgen toolkit v.2.0
crisprdo		0.7.15		✔Yes
cufflinks	Assembles transcripts, estimates their abundances, tests for differential expression and regulation in RNA-Seq samples	2.0.2		✔Yes		Genomics Toolkit
		2.1.1		✔Yes
		2.2.0		✔Yes
		2.2.1	✔Yes		✔Yes
cutadapt	Reads a FASTA or FASTQ file, finds and removes adapters, writes the changed sequence to standard output	1.11		✔Yes		Genomics Toolkit
		1.16	✔Yes		✔Yes
		1.1	✔Yes
		1.5			✔Yes
		1.9.1	✔Yes
cytoscape	Platform for visualizing complex-networks and integrating these with attribute data	3.6.1	✔Yes	✔Yes
Dammit	Simple de novo transcriptome annotator	0.3			✔Yes
deseq2	Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression	3.0.0		✔Yes
deepTools	Suite of python tools for the efficient analysis of high-throughput sequencing data	2.3.5			✔Yes
deepTools		3.1.3	✔Yes
Detonate	DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation	1.1			✔Yes
Diamond	Alignment tool for aligning short DNA sequencing reads to a protein reference database	0.7.11			✔Yes
		0.8.31			✔Yes
		0.8.3	✔Yes	✔Yes
		0.9.13	✔Yes
Dimspy	Processing of direct-infusion mass spectrometry-based metabolomics and lipidomics data	1.03	✔Yes
Discovar	Variant caller and small genome assembler	52488			✔Yes
Discovar de novo	Large (and small) de novo genome assembler	52488			✔Yes
discasm	Extract reads that map to reference genomes in a discordant fashion and optionally include reads that do not map to the genome at all, and perform a de novo transcriptome assembly of these reads	0.1.2	✔Yes
Drupal7	Drupal provides a back-end framework for at least 2.3% of all websites worldwide					Pop-up genome browser Harvesting Field Station Data Drupal Base
ECTools	Long read correction, plus other correction tools	12/1/2014			✔Yes
E-utilities	Table interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI)	6/24/2015				Mining SRA to identify datasets
EPA-ng	Perform maximum likelihood-based phylogenetic placement of genetic sequences	0.1.0-beta	✔Yes
edgeR	Differential expression analysis of RNA_seq expression profiles with biological replication	3		✔Yes
edge-pro	EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data.					Genomics Toolkit
eigensoft	Uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation	6.1.3		✔Yes
eigensoft		7.2.1		✔Yes
emboss	A high-quality package of free, Open Source software for molecular biology	6.5.7		✔Yes
emboss		6.6.0			✔Yes
EricScript	Computational framework for the discovery of gene fusions in paired end RNA-seq data.	0.5.5			✔Yes
ensembl	Various tools to assist in use and analysis of Ensembl data	95.1			✔Yes
evigene	Pipeline script for processing large piles of transcript assemblies, from several methods into the most biologically useful set of mRNA, classified into primary and alternate transcripts	2013.07.27	✔Yes
exonerate	Exonerate is a general purpose tool for biological sequence comparison	2.4	✔Yes		✔Yes
Falcon	Collection of genome assembly tools	0.4.1			✔Yes
fasta3	The FASTA package - protein and DNA sequence similarity searching and alignment programs					Genomics Toolkit
fastqc	Quality control for high-throughput sequence data	0.10.1		✔Yes		Arkansas Workshop Genomics Toolkit
		0.11.3			✔Yes
		0.11.5	✔Yes	✔Yes
FASTA-Splitter	Divides a single FASTA file into multiple files	0.2.4			✔Yes
FASTA-Splitter	Divides a single FASTA file into multiple files	0.1.2			✔Yes
fastx	A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing	0.0.13		✔Yes
fastx		0.0.14			✔Yes
flash	Fast and accurate tool to merge paired-end reads from NGS experiments	1.2.11		✔Yes	✔Yes
flexbar	Flexbar preprocesses high-throughput sequencing data efficiently	2.4		✔Yes
FragGeneScan	Finds fragmented genes in short reads and predicts prokaryotic genes in incomplete assemblies or complete genomes	1.2			✔Yes
Freebayes	Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs and complex events	1.2.0	✔Yes
gatk	Genome Analysis Toolkit, for high-throughput sequencing data	3	✔Yes			bcbio-nextgen toolkit v.2.0 Genomics Toolkit
		3.5			✔Yes
		3.6			✔Yes
		3.7			✔Yes
		4.0.1.2			✔Yes
		4.beta.5			✔Yes
Genome MuSiC	Tools to discover the significance of somatic mutations found in a cohort of cancer samples, and with respect to various external data sources	0.4.1			✔Yes
GFFRead	GFF/GTF parsing utility providing format conversions, region filtering, and FASTA sequence extraction	0.9.8 c			✔Yes
Glimmer	Gene Locator and Interpolated Markov ModelER to identify coding regions	3.0.2			✔Yes
Glimmer		3.0.4			✔Yes
GraPhlan	Tool for producing high quality circular representations of taxonomic and phylogenetic trees	0.9.7			✔Yes
gmap	Align cDNA to reference to determine gene structure and structural variants	5/15/2014		✔Yes
		4/4/2016		✔Yes
		6/20/2017	✔Yes
		5/11/201	✔Yes
gmapfusion	Identifying candidate fusion transcripts based on transcript sequences	0.3.0	✔Yes
guppy	Oxford Nanopore Technologies' basecalling algorithms	3.1.5-cpu	✔Yes
hisat2	Fast, sensitive alignment, mapping NGS reads (DNA & RNA) to a population of human genomes or against a single reference genome	0.1.6-beta		✔Yes		bcbio-nextgen toolkit v.2.0 Genomics Toolkit
		2.0.4		✔Yes	✔Yes
		2.1.0	✔Yes
hmmer	Biosequence analysis using profile hidden Markov models	3		✔Yes		Genome assembly workshop
		2.3.2
		3.1.b2	✔Yes		✔Yes
HUMAnN2	Pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomatic sequencing data	0.10.0			✔Yes
htseq	Analysis of high-throughput sequencing data using Python	0.9.1	✔Yes		✔Yes	bcbio-nextgen toolkit v.2.0
htslib	C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data	1.5	✔Yes
IDBA	Iterative De Bruijn Graph De Novo Assembler short read assembler for transcriptomes	1.1.1			✔Yes
IGV	The Integrative Genomics Viewer (IGV) is a high-performance visualization tool					Genomics Toolkit
ipython/Jupyter	Interactive python shell				✔Yes	bcbio-nextgen toolkit v.2.0
Ipyrad	Interactive toolkit for assembly and analysis of restriction-site associated genomic data sets â€“ RAD, RADseq, GBS	0.7.2	✔Yes
impute2	Estimating (imputing) unobserved genotypes in SNP association studies	2.2.2		✔Yes
Interproscan	Overview of the families that a protein belongs to and the domains sites in the sequences	5.29-6	✔Yes
Jellyfish/Jellyfish2	Tool for fast, memory efficient counting of k-mers in DNA	1.1.11			✔Yes	bcbio-nextgen toolkit v.2.0,
		2.2.6			✔Yes
		2.2.9	✔Yes
		2.2.10		✔Yes
Jbrowse	JBrowse is a fast, scalable genome browser built completely with JavaScript and HTML5.					Genomics Tookit Pop-up genome browser
kallisto	Quantifies abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads	0.42.3		✔Yes
		0.43.0		✔Yes	✔Yes
		0.43.1	✔Yes
khmer	Tools to work with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells	2.0.0			✔Yes
khmer		2.1.1	✔Yes
Kraken	System for assigning taxonomic labels to short DNA sequences	0.10.5			✔Yes	bcbio-nextgen toolkit v.2.0
		1			✔Yes
		2.0.7			✔Yes
ldhat	LDhat is a package of programs for the analysis of recombination from population genetic data	2.2		✔Yes
ldhot	LDhot is a package for inferring the location of recombination hotspots from patterns of linkage disequilibrium within samples	2014		✔Yes
limma	Data analysis, linear models and differential expression for expression data	3.0.0		✔Yes
lincrna	Identification, Characterization, and Quantification of Long Intergenic Non-Coding RNAs	1.0.0		✔Yes
Longranger	Analysis pipelines that processes Chromium sequencing (10X) output	2.1.6	✔Yes			Genome assembly workshop
Loupe	Loupe Cell Browser gene expression tutoria					Genome assembly workshop
mach	Markov Chain based haplotyper	1.0.1		✔Yes
macs	Model-based Analysis of ChIP-Seq, for identifying transcript factor binding sites	1.4.2		✔Yes		bcbio-nextgen toolkit v.2.0
		1.4.3			✔Yes
		2.1.0	✔Yes
		2.1.2	✔Yes
MACSE	Aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons	1.2			✔Yes
MAFFT	Multiple sequence alignment program	7.3			✔Yes
manta	Structural variant and indel caller for mapped sequencing data	1.4.0				Genomics Toolkit
maker	Ab initio gene predictions	2.31.10			✔Yes
maker	Ab initio gene predictions	2.31.9	✔Yes
mash	MinHash dimensionality-reduction technique for clustering abd searching massive sequence collections	2.1.1	✔Yes
masurca	Assembler combines the benefits of deBruijn graph and Overlap-Layout-Consensus assembly approaches.	3.2.0	✔Yes
		3.1.3			✔Yes
		3.2.2			✔Yes
		3.2.6			✔Yes
		3.2.7			✔Yes
mcl	Scalable unsupervised clustering algorithm	14-137	✔Yes
megahit	A single node assembler for large and complex metagenomics NGS reads, such as soil	1.1.2	✔Yes			Arkansas Workshop
megahit		1.1.1			✔Yes
MALT	MEGAN Alignment Tool, and extension of MEGAN	0.3.8			✔Yes
Mapsembler 2	Targeted assembly software	2.2.4			✔Yes
MaxBin	Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm	2.1.1			✔Yes
MEGAN	MEta Genome ANalyzer	5.11.3			✔Yes	MEGAN community edition
MEGAN	MEta Genome ANalyzer	6	✔Yes
metabat	Metagenome binning tool	2.11.3	✔Yes			Arkansas Workshop
Meraculous	Whole genome assembler for Next Generation Sequencing data geared for large genomes	2.2.4			✔Yes
MetaPhlAn	Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data	1.7.7			✔Yes
MetaPhlAn		2.6.0			✔Yes
MetaVelvet	Extension of Velvet assembler to de novo metagenome assembly from short sequence reads	1.2.10			✔Yes
Metapalette	k-mer based bacterial community reconstruction technique	1	✔Yes
migrate	Estimates effective population sizes and past migration rates between n population	3.3.2		✔Yes
mimar	Markov chain Monte Carlo method to estimate parameters of an isolation-migration model	12172010		✔Yes
MinCED	Program to find CRISPRs in full genomes or environmental datasets such as metagenomes	0.2.0			✔Yes
minia	Minia is a short-read assembler based on a de Bruijn graph	2.0.7	✔Yes
minimac	A low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation	11162012		✔Yes
mira	Assembler	4.0.2			✔Yes
mirdeep2	Discovers active known or novel miRNAs from deep sequencing data	0.1.2		✔Yes
miso	Mixture-of-Isoforms is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data	0.4.6		✔Yes
mothur	Bioinformatics tool for analyzing 16S rRNA gene sequences	1.31.2		✔Yes
		1.34.2		✔Yes
		1.38.1			✔Yes
		1.40.5	✔Yes
		1.41.3	✔Yes
mrbayes	MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models	3.2.1 mpi		✔Yes		Genomics Toolkit
mrbayes		3.2.6		✔Yes
mrsfast	mrsFAST is designed to map short reads to reference genome assemblies in a fast and memory-efficient manner	3.3.7		✔Yes
MUctect	Identification of somatic point mutations in next generation sequencing data of cancer genomes.					bcbio-nextgen toolkit v.2.0
MultiQC	Aggregate results from bioinformatics analyses across many samples into a single report					Genomics toolkit
mummer	System for rapidly aligning entire genomes, whether in complete or draft form	3.23	✔Yes	✔Yes	✔Yes
muscle	MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests	3.8.31	✔Yes	✔Yes	✔Yes
MyCC	Automated binning tool that visualizes metagenomes and identifies reconstructed genomic fragments	42341			✔Yes
nanopack	Long read processing and analysis	0.1.14	✔Yes
Nasp	Pipleine to identify SNP's in the data.	1.1.2	✔Yes
ngsutils	NGSUtils is a suite of software tools for working with next-generation sequencing datasets	0.5.2a		✔Yes
NGSCheckMate	Identifies NGS data files from the same individual	2016.10.12			✔Yes
ninja	Infers phylogeny using neighbor-joining tree	1.2.2		✔Yes
novoalign	Aligns short reads to reference genome for resequencing experiments	3. .0	✔Yes			bcbio-nextgen toolkit v.2.0
oases	De novo transcriptome assembler for very short reads	0.2.09	✔Yes
OpenRefine	Open source, power tool for working with messy data.					EML Workshop (private image)
paml	Phylogenetic analyses of DNA or protein sequences using maximum likelihood	4		✔Yes
paml		4.9		✔Yes	✔Yes
paup	Phylogenetic Analysis Using Parsimony is a computational phylogenetics program for inferring evolutionary trees	4	✔Yes	✔Yes
PBJELLY	Highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles	15.8.24			✔Yes	Genome assembly workshop
perl	Programming language				✔Yes	Arkansas Workshop,
phenix	For reference mapping, VCF genearation, VCF filtering, and SNP identification	4-Jan	✔Yes
phylip	PHYLogeny Inference Package	3.69	✔Yes	✔Yes	✔Yes
Phylosift	Tool suite to conduct phylogenetic analysis of genomes and metagenomes	1.0.1			✔Yes
picard	Manipulating high-throughput sequencing (HTS) data and formats.	2.14.0	✔Yes			Genomics Toolkit
		2.17.0			✔Yes
		2.1.1			✔Yes
		2.18.0			✔Yes
		2.20.2			✔Yes
Pilon	Automatically improves draft assemblies and finds variation among strains, including large event detection	1.16			✔Yes
Pilon		1.23	✔Yes
Platanus	De novo sequence assembler for NGS data	1.2.4			✔Yes
plink	Open-source C/C++ library for working with human genetic variation data	1.07		✔Yes
		2	✔Yes	✔Yes
		1.9		✔Yes
polyphen	Automatic tool for prediction of possible impact of an amino acid substitution on the structure and function of a human protein	2.2.2	✔Yes
Pplacer	Places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment	1.1.7			✔Yes
Primer3	PCR design tool	1.1.4
		2.2.3
		2.3.7
Prinseq	Quality control for high-throughput sequence data	1.2	✔Yes			Arkansas Workshop
Prokka	Software tool for rapid annotation of prokaryotic genomes	1.11			✔Yes
Prodigal	Fast, reliable protein-coding gene prediction for prokaryotic genomes	2.6.2			✔Yes
Prodigal		2.6.3			✔Yes
psi4	PSI4 provides a wide variety of quantum chemical methods using state-of-the-art numerical methods and algorithms	1.1	✔Yes		✔Yes
python	Programming language				✔Yes	Arkansas Workshop
QIIME2	Quantitative Insights Into Microbial Ecology	2.0.0				QIIME2
QUAST	Assembly evaluation tool	4.6.3	✔Yes			Arkansas Workshop Genome assembly workshop
QUAST	Assembly evaluation tool	5.0.0	✔Yes
R	Statistical computing and graphics	3.2.3			✔Yes	EML Workshop (private), R for Biologists Harvesting Field Station data
Rstudio	Open-source integrated development environment (IDE) for R, a programming language for statistical computing and graphics.	3.3.1			✔Yes
		3.3.3			✔Yes
		3.4.1			✔Yes
		3.5.1			✔Yes
		3.5.2			✔Yes
		3.6.0			✔Yes
r8s	Estimates absolute rates ('r s') of molecular evolution and divergence times on a phylogenetic tree	1		✔Yes
raxml	Maximum likelihood phylogeny estimation for interpreting relationships between sets of data	8.0.26		✔Yes		Genomics Toolkit
		8.2.11	✔Yes
		8.2.9			✔Yes
Raxml-ng	Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.	0.9.0	✔Yes
Raxml-ng		0.9.0-pthreads	✔Yes
Ray	Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data	2.3.1	✔Yes		✔Yes
reap	Estimating kinship coefficients and identify-by-descent (IBD) sharing probabilities in samples with admixed ancestry	1.2		✔Yes
repeatmasker	Screens DNA sequences for interspersed repeats and low complexity DNA sequences	4.0.7	✔Yes	✔Yes
repeatmasker		4.0.6			✔Yes
repeatmodeler	Screens DNA sequences for interspersed repeats and low complexity DNA sequences	4.0.6
		1.0.10	✔Yes
		1.0.		✔Yes
rmats	Computational tool to detect differential alternative splicing events from RNA-Seq data	3.2.5	✔Yes
rmats		4.0.2	✔Yes
RNAmmer	Predicts 5s/ s, 16s/1 s, and 23s/2 s ribosomal RNA in full genome sequences	1.2			✔Yes
rosetta	Software suite including algorithms for computational modeling and analysis of protein structures	3.5		✔Yes
		3.7			✔Yes
		3.8		✔Yes
		3.1	✔Yes
rsem	Estimates gene and isoform expression levels from RNA-Seq data	1.2.19		✔Yes
		1.2.21			✔Yes
		1.3.0	✔Yes
sailfish	Alignment-free isoform quantification from RNA-seq reads using lightweight algorithms	1.2.21
		0.7.3		✔Yes
		0.8.0		✔Yes
		0.9.2			✔Yes
salmon	Tool for fast transcript quantification from RNA-seq data	0.4.2		✔Yes		bcbio-nextgen toolkit v.2.0
		0.6.0			✔Yes	bcbio-nextgen toolkit v.2.0 Arkansas Workshop
		0.7.2			✔Yes
		0.8.1			✔Yes
		0.11.0	✔Yes	✔Yes
		0.9.1	✔Yes		✔Yes
samtools	Utilities for manipulating alignments in SAM format	1.3		✔Yes	✔Yes	Mining SRA to identify datasets Genomics Toolkit Genome assembly workshop
		1.3.1			✔Yes
		1.5	✔Yes
		0.1.1		✔Yes
		1.9	✔Yes		✔Yes
		0.1.19
		1.2		✔Yes
		1.7			✔Yes
Seqtk	Toolkit for processing sequences in FASTA/Q formats	1.2-r94			✔Yes
SignalP	Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes and eukaryotes	4.1c			✔Yes
skmer	Estimating distances between genomes from low-coverage sequencing reads	3.0.1	✔Yes
SNVMIX	Detects single nucleotide variants from next generation sequencing data	0.11.8-r5			✔Yes
smrt	Automated and distributed secondary analysis of sequencing data generated by the PacBio single-molecule, real-time (SMRT) sequencing system	2.2.0		✔Yes		PacBio SMRT analysis
		5.1.0			✔Yes
		7.0.1			✔Yes
somaticsniper	SomaticSniper is a program to identify single nucleotide positions that are different between tumor and norma	1.0.5			✔Yes
soapdenovo	De novo assembler for next generation sequencing reads	r240		✔Yes
		9/10/2015			✔Yes
		2.04	✔Yes
soapdenovotrans	A de novo transcriptome assembler inherited from the SOAPdenovo2 framework, designed for assembling transcriptome with alternative splicing and different expression level	1.03	✔Yes
solar eclipse	SOLAR-Eclipse is an extensive, flexible software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening	.3.1		✔Yes		bcbio-nextgen toolkit v.2.0
spades	St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies	3.10.1	✔Yes	✔Yes	✔Yes	Genomics Toolkit
		3.11.1	✔Yes		✔Yes
		3.8.1			✔Yes
		3.8.2		✔Yes
		3.9.0		✔Yes
spm	Statistical Parametric Mapping		✔Yes	✔Yes
spm	Statistical Parametric Mapping	12	✔Yes	✔Yes
sra-toolkit	Collection of tools and libraries for using data in the INSDC Sequence Read Archives	2.3.5-2		✔Yes		Mining SRA to identify datasets
		2.5.4		✔Yes
		2.8.1			✔Yes
		2.8.2	✔Yes
		2.9.1			✔Yes
stacks	A modular pipeline for building loci from short-read sequences	1.4	✔Yes
star	Spliced Transcripts Alignment to a Reference	2.5.3	✔Yes			Genomics Toolkit
		2.6.1a	✔Yes
		2.4.1		✔Yes
		2.5.2		✔Yes	✔Yes
		1.3.3b
		2.5.4			✔Yes
		2.7.0			✔Yes
Strelka	Somatic variant calling workflow for matched tumor-normal samples	1.0.01			✔Yes
starfusion	Spliced Transcripts Alignment to a Reference	1.1.0	✔Yes		✔Yes
		1.3.1			✔Yes
		1.5.0			✔Yes
stringtie	Fast and highly efficient assembler of RNA sequence alignments into potential transcripts	1.3.3b	✔Yes		✔Yes	Genomics Toolkit
Supernova	Supernova is a software package from 10X Genomics for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source	0.2.6				Genome assembly workshop
tabix	Tabix works on generic tabular data formats for genomic information, quickly retrieving features overlapping specified areas on the genome	0.26	✔Yes	✔Yes		Genomics Toolkit
Tcoffee	Multiple Sequence Alignment Server					Genomics Toolkit
Theano	Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently	0.8.0			✔Yes
Theano		0.8.2			✔Yes
TMHMM	Predicts transmembrane helices in proteins	2			✔Yes	bcbio-nextgen toolkit v.2.0
tophat	Fast splice junction mapper for RNA-Seq reads	2.0.7		✔Yes		Genomics Toolkit
		2.1.0		✔Yes	✔Yes
		2.1.1	✔Yes		✔Yes
tophat2	Splice junction mapper for RNA-Seq reads	4.6.2				bcbio-nextgen toolkit v.2.0,
		3.14
		2.1.1	✔Yes
transabyss	Analysis for ABySS-assembled contigs from shotgun transcriptome data for finding splice sites and variants	1.0.3
		1.5.5	✔Yes
		2.0.1	✔Yes		✔Yes
transdecoder	TransDecoder identifies candidate coding regions within transcript sequences	0.5.1
		0.4.5
		3.0.1			✔Yes
Transrate	Software for de-novo transcriptome assembly quality analysis	1.0.3	✔Yes		✔Yes
trim galore	A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files	2.1.1				Arkansas Workshop
		0.4.5	✔Yes		✔Yes
		0.6.3			✔Yes
trimmomatic	Fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters.	0.36	✔Yes	✔Yes	✔Yes	Genomics Toolkit
trimmomatic		0.35		✔Yes
trinity	Package which enables the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data	2.3.2			✔Yes	Arkansas Workshop
		2.4.0	✔Yes	✔Yes	✔Yes
		2.0.1
		2.6.6	✔Yes
		2.8.4	✔Yes	✔Yes	✔Yes
		2.1.1		✔Yes	✔Yes
		2.0.6			✔Yes
		2.2.0			✔Yes
Trinotate	Annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms	3.1.1	✔Yes		✔Yes
Trinotate		2.0.2			✔Yes
Tombo	Modified nucleotides from nanopore sequencing data	1.5	✔Yes
vcftools	Tool providing easily accessible methods for working with complex genetic variation data in the form of VCF files	0.1.14		✔Yes		bcbio-nextgen toolkit v.2.0 Genomics Toolkit
		0.1.13	✔Yes	✔Yes
		1.2.10
		0.1.10		✔Yes
		0.1.17			✔Yes
		0.1.15			✔Yes
velvet	De novo genomic assembler specially designed for short read sequencing technologies	1.21	✔Yes		✔Yes
warbleR	Bioacoustics research encompasses a wide range of questions, study systems and methods, including the software used for analyses.					Harvesting Field Station Data

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