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BioHPC Cloud:
: Software

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NameVersionOSAboutInstalledUpdatedMore
3d-dna08012019Linux3D de novo assembly (3D-DNA) pipeline4/21/2021 detailed information
454 gsAssembler or gsMapper2.8LinuxAssembly and alignment software for 454 or other long reads.12/13/20113/24/2014detailed information
a520150522LinuxA genome assembly pipeline for bacteria and archaea10/14/20136/3/2016detailed information
ABRicatev1.0.0LinuxMass screening of contigs for antimicrobial resistance or virulence genes. 6/11/20182/16/2023detailed information
ABruijn20161221LinuxABruijn is a de novo assembler for PacBio and Oxford Nanopore Technologies reads. 12/21/2016 detailed information
ABySS 2.2.5LinuxIllumina short reads assembly tool.12/13/20119/25/2020detailed information
AdapterRemoval2.1.1LinuxRemove adapters from sequences in either single end or paired end experiments9/16/2015 detailed information
adephylo20190401LinuxMultivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.4/1/2019 detailed information
Admixtools5.1LinuxThe ADMIXTOOLS package implements 5 methods described in Patterson et al (2012) Ancient Admixture in Human History.11/6/201312/20/2018detailed information
Admixture1.3.0LinuxSoftware tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.2/19/20149/24/2020detailed information
AFProfile20230713LinuxProtein complex prediction with AlphaFold-multimer by denoising the MSA profile.8/30/2023 detailed information
agrep3.41.5Linuxapproximate GREP for fast fuzzy string searching.7/12/2018 detailed information
albacore2.3.4LinuxNanopore base caller.6/2/20171/4/2019detailed information
Alder1.03LinuxThe ALDER software computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture.11/6/201311/6/2013detailed information
AliTV-Perl interface1.0.6LinuxAliTV-Perl interface11/29/2022 detailed information
AlleleSeq1.1LinuxDetects SNVs from ChIP-seq or RNA-seq experiments.4/2/2014 detailed information
ALLMAPS20150710LinuxALLMAPS is capable of computing a scaffold ordering that maximizes the colinearity to a collection of maps, including genetic, physical or comparative maps into the final chromosome build.7/10/2015 detailed information
ALLPATHS-LG52415LinuxIllumina short reads assembly tool.12/14/20111/9/2018detailed information
Alphafold2.3.2LinuxProtein structure prediction.7/27/20217/8/2023detailed information
AMOS3.1.0LinuxAMOS is a collection of tools and class interfaces for the assembly of DNA reads. 1/12/20131/14/2013detailed information
AMPHORA2LinuxAMPHORA is an Automated Phylogenomic Inference Pipeline for bacterial sequences7/26/20177/27/2017detailed information
amplicon.py1LinuxCall haplotype variants using amlicon sequencing data8/6/2019 detailed information
AMRFinder3.11.2LinuxNCBI Antimicrobial Resistance Gene Finder4/8/20202/7/2023detailed information
analysis0.8.4Linux C++ software for evolutionary genetic analysis.9/2/2014 detailed information
ANGSD0.940LinuxANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities.3/27/201510/20/2022detailed information
Annovar20130823LinuxSNP/INDEL annotation.12/13/20111/22/2015detailed information
ant1.9.9LinuxApache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. 11/30/2021 detailed information
antiSMASH5.0.0LinuxantiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.12/1/201711/27/2019detailed information
anvio7.1LinuxIntegrated multi-omics at scale7/30/20206/6/2022detailed information
apollo20170925LinuxManual genome annotation9/25/2017 detailed information
arcs1.1.1LinuxScaffold genome sequence assemblies using linked read sequencing data6/11/2020 detailed information
ARGweaver1.0LinuxEstimating Ancestral recombination graphs12/4/2020 detailed information
aria21.36.0LinuxFast download utility7/4/2023 detailed information
ariba2.14.6LinuxAntimicrobial Resistance Identification By Assembly2/8/2023 detailed information
Arlequin3.5.2.2LinuxAn Integrated Software for Population Genetics Data Analysis10/31/2017 detailed information
ART2016.06.05LinuxA set of simulation tools to generate synthetic next-generation sequencing reads. 1/15/2021 detailed information
ASEQ1.1.11LinuxFast allele-specific studies from next-generation sequencing data5/4/2023 detailed information
aspera4.2.3.197LinuxIBM Aspera Connect is an install-on-demand application that facilitates high-speed uploads and downloads with an Aspera transfer server.10/12/201812/7/2022detailed information
assembly-stats1.0.1LinuxGet assembly statistics from FASTA and FASTQ files.4/14/2019 detailed information
ASTRAL5.15.3LinuxEstimating an unrooted species tree given a set of unrooted gene trees.2/2/2021 detailed information
atac-seq-pipeline2.1.1LinuxThis pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data. 10/27/20182/24/2022detailed information
ataqv1.2.1LinuxATAC-seq QC and visualization1/13/2021 detailed information
athena_meta1.1LinuxAthena is a read cloud assembler for metagenomes.1/30/2019 detailed information
ATLAS1.0LinuxAnalysis tools for low-coverage and ancient DNA samples5/17/2019 detailed information
Atlas-Link2050709LinuxAtlas-Link links and orients genome sequence contigs quickly and accurately using mate-pair information.7/9/2015 detailed information
ATLAS_GapFill2.2LinuxATLAS GapFill deals with the repetitive gap assembly problem by using the unique gap-flanking sequences to group reads and convert the problem to a local assembly task.7/9/2015 detailed information
atom1.50.0Linuxtext editor8/25/2020 detailed information
ATSAS 2.5.0-2LinuxA program suite for small-angle scattering data analysis from biological macromolecules.12/13/20111/31/2013detailed information
Augustus3.4.0LinuxAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences1/23/20131/2/2022detailed information
AWS command line interface1.19.41LinuxProvides command-line access to Amazon Web Services2/15/20183/31/2021detailed information
AWS v2 Command Line Interface2.1.32LinuxThe AWS Command Line Interface (AWS CLI) is an open source tool that enables you to interact with AWS services using commands in your command-line shell. 4/2/2021 detailed information
axe0.3.2LinuxRapid competitive read demulitplexer. 3/5/2018 detailed information
axel2.17.10Linuxaccelerate the download process by using multiple connections per file6/3/2021 detailed information
BactSNP1.1.0LinuxBactSNP is a tool to identify SNPs among bacterial isolates. 6/13/2019 detailed information
bakta1.7.0LinuxAnnotation of bacterial genomes & plasmids12/9/20205/19/2023detailed information
bam2fastx1.3.0LinuxConversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data8/6/2019 detailed information
bamsurgeon1.4.1LinuxAdding genomic variants to SAM/BAM/CRAM files, used for testing variant callers1/17/2023 detailed information
bamtools2.5.2LinuxBAM file processing and filtering.12/13/20119/5/2023detailed information
bamUtil1.0.14LinuxbamUtil is a repository that contains several programs that perform operations on SAM/BAM files.1/17/2019 detailed information
barcode_splitter0.18.6LinuxA utility to split multiple sequence files using multiple sets of barcodes.4/12/2022 detailed information
BarNone1.0LinuxMatching and counting sequencing barcodes (e.g., from Bar-Seq) to a catalog. Inexact matching via minimum Levenshtein distance.1/13/2020 detailed information
Basset0.1.0LinuxDeep convolutional neural networks for DNA sequence analysis.5/15/2017 detailed information
BayeScan2.1LinuxBayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.11/24/2014 detailed information
Bayescenv 1.1LinuxBayeScEnv is genome-scan software: it aims at detecting local adaptation linked to a given environmental variable using medium- to high-density genotypic data. 6/19/2018 detailed information
bayesR20210104LinuxBayesian hierarchical model for complex trait analysis9/18/2023 detailed information
baypass2.2Linuxpopulation genomics software which is primarily aimed at identifying genetic markers subjected to selection and/or associated to population-specific covariates (e.g., environmental variables, quantitative or categorical phenotypic characteristics). 9/23/2020 detailed information
bazel5.1.0LinuxBuild and test software3/28/2022 detailed information
BBMap/BBTools39.01LinuxThe BBTools package includes BBMap, a short read aligner, and various other useful bioinformatic tools11/6/201510/17/2022detailed information
BCFtools1.18Linuxbcftools — utilities for variant calling and manipulating VCFs and BCFs.2/20/20178/10/2023detailed information
bcl2fastq2.20.0Linuxbcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.8/7/201711/14/2017detailed information
BCP1.1LinuxBayesian Change-point Model (BCP) is a method for analysis different type of ChIP-seq data.10/23/2017 detailed information
Beagle5.0LinuxPhasing, imputation, Haplotype inferrance11/18/20131/2/2019detailed information
Beast22.6.7LinuxBEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.3/27/20175/26/2022detailed information
bedops2.4.35LinuxFast BED file operaion.7/26/20134/25/2019detailed information
BEDtools2.29.2LinuxBED file operation.2/6/20121/14/2020detailed information
bfc20150417LinuxHigh-performance error correction for Illumina resequencing data10/18/2016 detailed information
bgc1.01Linuxbgc implements Bayesian estimation of genomic clines to quantify introgression at many loci.2/12/20132/12/2013detailed information
bgen20180807LinuxBGEN: a binary file format for imputed genotype and haplotype data11/30/2018 detailed information
bigQF1.3-1LinuxR package for large quadratic forms2/26/2018 detailed information
bigWig20171211LinuxR library to work with UCSC bigwig files12/11/2017 detailed information
bioawk20180714LinuxBioawk is an extension to Brian Kernighan's awk7/24/2018 detailed information
biobakeryv3.0.0a7LinuxMicrobial community profiling12/14/2021 detailed information
biobambam0.0.125LinuxThis package contains tools for processing BAM files.2/28/20142/28/2014detailed information
Bioconductor3.0LinuxR package for genomics data analysis.7/19/20133/24/2014detailed information
biom-format20180521LinuxThe BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. 5/21/2018 detailed information
BioPerl1.7.8LinuxPERL library for general bioinformatics.12/13/201110/30/2022detailed information
BioPython1.60Linux 2/27/20121/31/2013detailed information
Birdsuite1.5.5LinuxSet of tools to detect and report SNP genotypes, common CNPs, and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform.4/11/2014 detailed information
Bismark0.24.1LinuxA bisulfite read mapper and methylation caller 11/20/20126/16/2023detailed information
Blackbird2019-11-25LinuxSV detection with 10X reads8/23/2022 detailed information
blasr20180816LinuxThe PacBio long read aligner9/24/20148/16/2018detailed information
BLAST2.13.0LinuxSequence alignment.12/13/20112/15/2023detailed information
BLAST_to_BED20200928LinuxParses a BLAST XML file and creates a BED file9/28/2020 detailed information
blast2goDB: August.2022: Software: v1.5.1LinuxGene Ontology annotation and function enrichment analysis.4/15/20135/19/2021detailed information
BLAT34LinuxSequence alignment.12/13/20115/1/2012detailed information
BlobToolKit2.6.3LinuxVisualisation, quality control and taxonomic partitioning of genome datasets9/30/2021 detailed information
BLUPF902019.04.23LinuxFortran 90/95 software for mixed model computations in animal breeding5/8/2019 detailed information
BMGE1.12LinuxSelection of phylogenetic informative regions from multiple sequence alignments3/9/2018 detailed information
bmtagger2/21/14LinuxBest Match Tagger for removing human reads from metagenomics datasets10/6/2016 detailed information
bonito0.6.1LinuxA PyTorch Basecaller for Oxford Nanopore Reads.9/22/2022 detailed information
Boost1.80.0LinuxBoost provides free peer-reviewed portable C++ source libraries.12/17/201411/5/2022detailed information
Bowtie1.1.2LinuxAn ultrafast, memory-efficient short read aligner.12/13/20113/22/2016detailed information
Bowtie22.5.1LinuxAn ultrafast, memory-efficient short read aligner.5/1/20128/15/2023detailed information
BPGA1.3LinuxComprehensive pan genome analysis of microorganisms10/25/2017 detailed information
Bracken2.8LinuxA companion program to Kraken 1.0 or Kraken 2.0.2/12/20198/7/2023detailed information
BRAKER2.1.6LinuxUses genomic and RNA-Seq data to automatically generate full gene structure annotations in novel genome9/1/20195/20/2021detailed information
BRAT-NextGen20150505LinuxNextGen software for Bayesian analysis of recombinations in whole-genome DNA sequence data,2/27/2019 detailed information
BRBseqTools1.6LinuxA suite of tools for the pre-processing of BRB-seq data (bulk RNA-seq)7/5/2022 detailed information
BreedingSchemeLanguage20180424LinuxWe present here a simple and flexible simulation platform, the breeding scheme language (BSL)4/24/2018 detailed information
breseq0.32.1Linuxbreseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for haploid microbial-sized genomes. breseq is a command line tool implemented in C++ and R. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads (such as those produced by new mobile element insertions) in an annotated HTML format.6/29/20167/9/2018detailed information
brocc1.4.0LinuxGenerate consensus-based taxonomic assignments from BLAST results.1/4/2019 detailed information
bsmap2.74Linuxa short reads mapping program for bisulfite sequencing in DNA methylation study6/24/2023 detailed information
BSseeker22.1.0LinuxMapping the bisulfite-treated short reads1/23/2017 detailed information
BUSCO5.5.0LinuxAssessing genome assembly and annotation completeness.1/22/20168/31/2023detailed information
BWA0.7.17LinuxBWA is a software package for mapping low-divergent sequences against a large reference genome.12/13/20114/25/2019detailed information
bwa-mem22.2.1LinuxBwa-mem2 is the next version of the bwa-mem algorithm in bwa.9/26/2022 detailed information
bwa-methv0.2.0Linuxaligners for BS-Seq1/17/2018 detailed information
bwtool1.0LinuxA command-line utility for bigWig files1/26/2022 detailed information
cactus2.6LinuxCactus is a reference-free whole-genome multiple alignment program10/9/20187/24/2023detailed information
CAFE4.2.1LinuxAnalysis of gene Family Evolution12/3/2019 detailed information
caffe1.0LinuxA deep learning framework made with expression, speed, and modularity in mind11/28/2022 detailed information
cagee1.1LinuxComputational Analysis of Gene Expression Evolution11/21/20224/3/2023detailed information
canu2.2Linuxassemble pacbio or nanopore reads2/11/201611/17/2022detailed information
CAP312/21/07LinuxA DNA Sequence Assembly Program4/4/2014 detailed information
caper1.5.1LinuxCromwell Assisted Pipeline ExecutoR5/4/2021 detailed information
CarveMe1.5.2LinuxConstructs a universal draft model of metabolism by downloading all reactions and metabolites in the BiGG database into a single SBML file. CarveMe can automates curation tasks to build a final universal model. It is based on a universal biomass equation and offers no blocked or unbalanced reactions. This tool can be used to create microbial community models by merging selected sets of single-species models into community-scale networks.8/28/20198/4/2023detailed information
catch1.4.0LinuxCompact Aggregation of Targets for Comprehensive Hybridization9/22/2021 detailed information
cBar1.2LinuxDistinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data11/1/2017 detailed information
CBSU RNAseq1.0Linux 12/13/20115/1/2012detailed information
CCMetagen1.4LinuxCCMetagen processes sequence alignments produced with KMA.1/12/2022 detailed information
CCTpack20181009LinuxConsensus analysis, model-based clustering, and cultural consensus theory applications to response data (e.g. questionnaires).10/9/2018 detailed information
cd-hit4.8.1Linuxcluster reads based on sequence similarity9/28/20157/21/2020detailed information
cdbfasta20191012LinuxIndexing and retrieval tools for FASTA files10/13/2019 detailed information
CEGMA2.5LinuxCEGMA (Core Eukaryotic Genes Mapping Approach) is a tool for building a highly reliable set of gene annotations in the absence of experimental data.1/16/2015 detailed information
CellRanger7.1.0LinuxA set of analysis pipelines that perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.5/15/20179/5/2023detailed information
cellranger-arc1.0.1LinuxA set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage.12/10/2020 detailed information
cellranger-atac2.1.9LinuxSet of analysis pipelines that process Chromium Single Cell ATAC data4/1/201910/2/2023detailed information
cellranger-dna1.1.0Linuxet of analysis pipelines that process Chromium single cell DNA sequencing output3/8/20203/8/2020detailed information
centrifuge20171218LinuxMicrobial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. 12/18/2017 detailed information
centroFlye20200709LinuxCentromere assembly using long error-prone reads7/9/2020 detailed information
CFM-ID2LinuxProcessing of EI-MS (GC-MS) and ESI-MS/MS (LC-MS) data for identification of metabolites.10/18/2019 detailed information
CFSAN SNP pipeline 2.2.1LinuxSNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. 2/6/20183/30/2021detailed information
CheckM1.2.2LinuxCheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes10/11/20162/18/2023detailed information
CheckM21.0.1LinuxRapid assessment of genome bin quality using machine learning.5/31/2023 detailed information
chimera1.16LinuxInteractive visualization and analysis of molecular structures and related data.3/17/20192/6/2023detailed information
chimerax1.6.1LinuxMolecular visualization program8/31/2023 detailed information
chip-seq-pipeline2.1.6LinuxENCODE Transcription Factor and Histone ChIP-Seq processing pipeline6/2/2022 detailed information
chromosomerchromosomerLinuxChromosomer is a reference-assisted assembly tool for producing draft chromosome sequences.6/18/2018 detailed information
Circlator1.5.5LinuxA tool to circularize genome assemblies4/8/2018 detailed information
Circos0.67-7LinuxCircos is a software package for visualizing data and information.3/24/2015 detailed information
Circuitscape4.0.5LinuxAn open-source program that uses circuit theory to model connectivity in heterogeneous landscapes4/16/2015 detailed information
CITE-seq-Count1.4.5LinuxCount antibody TAGS from a CITE-seq and/or cell hashing experiment.5/14/20209/18/2023detailed information
ClermonTyping20220304LinuxEscherichia genus strain phylotyping3/4/2022 detailed information
clues20201201LinuxInferring selection and allele frequency trajectories from DNA sequence data12/1/2020 detailed information
CLUMPP1.1.2LinuxCLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses.4/10/2017 detailed information
clust1.18.0LinuxOptimised consensus clustering of one or more heterogeneous datasets.11/27/20196/22/2023detailed information
Clustal Omega1.2.4LinuxMultiple sequence alignment2/24/20154/25/2019detailed information
CLUSTALW2.1LinuxGeneral purpose DNA or protein multiple sequence alignment program for three or more sequences.12/13/20115/1/2012detailed information
Cluster1.52LinuxThe open source clustering software implementing the most commonly used clustering methods for gene expression data analysis.4/28/2014 detailed information
cmake3.22.0-rc1LinuxCMake is an open-source, cross-platform family of tools designed to build, test and package software5/22/201710/20/2021detailed information
CMSeq1.0.4LinuxCMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus.8/23/2022 detailed information
CNVnator0.4.1LinuxA tool for CNV discovery and genotyping from depth of read mapping6/23/20159/5/2023detailed information
coinfinder1.2.0Linuxdetects genes which associate and dissociate with other genes more often than expected by chance in pangenomes4/4/2023 detailed information
colabfold1.3.0Linuxa variation of alphafold12/5/2022 detailed information
compat0.8LinuxThe compat program takes a file in Phylip alignment format (non-interlaced) or fasta format as input. It produces one or more output files containing phylogenetic trees4/5/2018 detailed information
CONCOCT1.1.0LinuxA program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.3/20/201811/1/2019detailed information
Conda20181201LinuxAn open source package management system and environment management system.12/2/2018 detailed information
Cooler0.8.11LinuxScalable quantitative maps.6/30/2021 detailed information
copyNumberDiff20200708Linuxcompare two groups of individuals to see if there are copy number differences the correlate with group assignment. 5/21/20187/8/2020detailed information
cortex_var1.0.5.21Linuxcortex_var is a tool for genome assembly and variation analysis from sequence data. 7/18/2017 detailed information
CoverMv0.6.1LinuxDNA read coverage and relative abundance calculator focused on metagenomics applications.2/9/2022 detailed information
CRISPRCasFinder4.2.20LinuxThe CRISPRCasFinder program enables the easy detection of CRISPRs and cas genes in user-submitted sequence data10/4/201812/20/2021detailed information
CRISPResso1.0.13LinuxCRISPResso is a software pipeline for the analysis of targeted CRISPR-Cas9 sequencing data.11/12/2018 detailed information
Cromwell85LinuxWorkflow Management System geared towards scientific workflows. Cromwell is open sourced under the BSD 3-Clause license.2/28/2023 detailed information
CrossMap0.6.1LinuxCrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies.5/11/201610/21/2022detailed information
CRT LinuxCRISPR Recognition Tool3/24/2017 detailed information
cuda8.0.61LinuxA parallel computing platform and programming model invented by NVIDIA.5/15/2017 detailed information
Cufflinks2.2.1LinuxRNA-seq reference guided transcript assembly, quantification and differential expressed gene identification12/13/20115/6/2014detailed information
cutadapt4.1Linuxcutadapt removes adapter sequences from high-throughput sequencing data.10/11/20139/7/2022detailed information
cuteSV1.0.10LinuxSensitive, fast, and scalable long-read-based SV detection4/22/2021 detailed information
dadi2.1.0LinuxIt implements a method for demographic inference from genetic data, based on a diffusion approximation to the allele frequency spectrum.5/12/20158/11/2020detailed information
dadi-1.6.3_modif1.6.3_modLinuxModified Dadi software6/7/2017 detailed information
danpos2.2.2LinuxA toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing7/21/2019 detailed information
DAS_Tool1.1.6LinuxDAS Tool for genome resolved metagenomics1/10/2023 detailed information
DBSCAN-SWA20201025LinuxAn integrated tool for rapid prophage detection and annotation10/25/2022 detailed information
dDocent2.8.13Linuxsimple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing.8/29/20178/9/2021detailed information
DeconSeq0.4.3LinuxDECONtamination of SEQuence data using a modified version of BWA-SW11/6/2015 detailed information
Deepbinner0.2.0LinuxDemultiplexing barcoded Oxford Nanopore sequencing reads.11/25/2019 detailed information
DeepTE20200521LinuxClassify transposons with unknown classification via Convolutional Neural Network.5/21/2020 detailed information
deepTools3.5.1LinuxA suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data.10/14/20161/28/2022detailed information
defusion20180531LinuxA tool to entangle MAKER fused genome annotation5/31/2018 detailed information
delly0.8.7LinuxDELLY is an integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. 11/13/20131/21/2021detailed information
DESMAN2.1LinuxDe novo Extraction of Strains from MetAgeNomes8/13/2019 detailed information
destruct1.1Linuxdistruct is a program that can be used to graphically display results produced by the genetic clustering program structure or by other similar programs.4/10/2017 detailed information
DETONATE1.10LinuxBoth packages are mainly intended to be used to evaluate de novo transcriptome assemblies2/16/2016 detailed information
diamond2.1.1LinuxAccelerated BLAST compatible local sequence aligner11/24/20142/18/2023detailed information
diploSHIC20210402LinuxdiploS/HIC uses a deep convolutional neural network to identify hard and soft selective sweep in population genomic data.10/29/20184/2/2021detailed information
discoal0.1.4Linuxdiscoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples7/11/2019 detailed information
Discovar52488LinuxDISCOVAR is a small genome assembler and variant caller from Broad Institute. Uses 250pb PE PCR-free Illumina reads.8/11/20142/12/2016detailed information
Discovar de novo52488LinuxExperimental de novo assembler for large genomes using 250pb PE PCR-free Illumina reads. From Broad Institute.8/11/20142/12/2016detailed information

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