Name | Version | OS | About | Installed | Updated | More |
454 gsAssembler or gsMapper | 2.8 | Linux | Assembly and alignment software for 454 or other long reads. | 12/13/2011 | 3/24/2014 | detailed information |
a5 | 20150522 | Linux | A genome assembly pipeline for bacteria and archaea | 10/14/2013 | 6/3/2016 | detailed information |
ABRicate | v0.8 | Linux | Mass screening of contigs for antimicrobial resistance or virulence genes. | 6/11/2018 | | detailed information |
ABruijn | 20161221 | Linux | ABruijn is a de novo assembler for PacBio and Oxford Nanopore Technologies reads. | 12/21/2016 | | detailed information |
ABySS | 2.2.5 | Linux | Illumina short reads assembly tool. | 12/13/2011 | 9/25/2020 | detailed information |
AdapterRemoval | 2.1.1 | Linux | Remove adapters from sequences in either single end or paired end experiments | 9/16/2015 | | detailed information |
adephylo | 20190401 | Linux | Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. | 4/1/2019 | | detailed information |
Admixtools | 5.1 | Linux | The ADMIXTOOLS package implements 5 methods described in Patterson et al (2012) Ancient Admixture in Human History. | 11/6/2013 | 12/20/2018 | detailed information |
Admixture | 1.3.0 | Linux | Software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. | 2/19/2014 | 9/24/2020 | detailed information |
agrep | 3.41.5 | Linux | approximate GREP for fast fuzzy string searching. | 7/12/2018 | | detailed information |
albacore | 2.3.4 | Linux | Nanopore base caller. | 6/2/2017 | 1/4/2019 | detailed information |
Alder | 1.03 | Linux | The ALDER software computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture. | 11/6/2013 | 11/6/2013 | detailed information |
AlleleSeq | 1.1 | Linux | Detects SNVs from ChIP-seq or RNA-seq experiments. | 4/2/2014 | | detailed information |
ALLMAPS | 20150710 | Linux | ALLMAPS 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-LG | 52415 | Linux | Illumina short reads assembly tool. | 12/14/2011 | 1/9/2018 | detailed information |
AMOS | 3.1.0 | Linux | AMOS is a collection of tools and class interfaces for the assembly of DNA reads. | 1/12/2013 | 1/14/2013 | detailed information |
AMPHORA | 2 | Linux | AMPHORA is an Automated Phylogenomic Inference Pipeline for bacterial sequences | 7/26/2017 | 7/27/2017 | detailed information |
amplicon.py | 1 | Linux | Call haplotype variants using amlicon sequencing data | 8/6/2019 | | detailed information |
AMRFinder | 3.6.15 | Linux | NCBI Antimicrobial Resistance Gene Finder | 4/8/2020 | | detailed information |
analysis | 0.8.4 | Linux | C++ software for evolutionary genetic analysis. | 9/2/2014 | | detailed information |
ANGSD | 0.931-4-g10d2f2b | Linux | ANGSD 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. | 3/27/2015 | 10/2/2019 | detailed information |
Annovar | 20130823 | Linux | SNP/INDEL annotation. | 12/13/2011 | 1/22/2015 | detailed information |
antiSMASH | 5.0.0 | Linux | antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. | 12/1/2017 | 11/27/2019 | detailed information |
anvio | 6.2 | Linux | Integrated multi-omics at scale | 7/30/2020 | | detailed information |
apollo | 20170925 | Linux | Manual genome annotation | 9/25/2017 | | detailed information |
arcs | 1.1.1 | Linux | Scaffold genome sequence assemblies using linked read sequencing data | 6/11/2020 | | detailed information |
ARGweaver | 1.0 | Linux | Estimating Ancestral recombination graphs | 12/4/2020 | | detailed information |
Arlequin | 3.5.2.2 | Linux | An Integrated Software for Population Genetics Data Analysis | 10/31/2017 | | detailed information |
ART | 2016.06.05 | Linux | A set of simulation tools to generate synthetic next-generation sequencing reads. | 1/15/2021 | | detailed information |
aspera | 3.9.9 | Linux | IBM Aspera Connect is an install-on-demand application that facilitates high-speed uploads and downloads with an Aspera transfer server. | 10/12/2018 | 3/13/2020 | detailed information |
assembly-stats | 1.0.1 | Linux | Get assembly statistics from FASTA and FASTQ files. | 4/14/2019 | | detailed information |
ASTRAL | 5.15.3 | Linux | Estimating an unrooted species tree given a set of unrooted gene trees. | 2/2/2021 | | detailed information |
atac-seq-pipeline | 1.7.0 | Linux | This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data. | 10/27/2018 | 4/6/2020 | detailed information |
ataqv | 1.2.1 | Linux | ATAC-seq QC and visualization | 1/13/2021 | | detailed information |
athena_meta | 1.1 | Linux | Athena is a read cloud assembler for metagenomes. | 1/30/2019 | | detailed information |
ATLAS | 1.0 | Linux | Analysis tools for low-coverage and ancient DNA samples | 5/17/2019 | | detailed information |
Atlas-Link | 2050709 | Linux | Atlas-Link links and orients genome sequence contigs quickly and accurately using mate-pair information. | 7/9/2015 | | detailed information |
ATLAS_GapFill | 2.2 | Linux | ATLAS 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 |
atom | 1.50.0 | Linux | text editor | 8/25/2020 | | detailed information |
ATSAS | 2.5.0-2 | Linux | A program suite for small-angle scattering data analysis from biological macromolecules. | 12/13/2011 | 1/31/2013 | detailed information |
Augustus | 3.3.3 | Linux | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences | 1/23/2013 | 10/13/2019 | detailed information |
AWS command line interface | 1.19.41 | Linux | Provides command-line access to Amazon Web Services | 2/15/2018 | 3/31/2021 | detailed information |
AWS v2 Command Line Interface | 2.1.32 | Linux | The 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 |
axe | 0.3.2 | Linux | Rapid competitive read demulitplexer. | 3/5/2018 | | detailed information |
BactSNP | 1.1.0 | Linux | BactSNP is a tool to identify SNPs among bacterial isolates. | 6/13/2019 | | detailed information |
bakta | 0.4 | Linux | Annotation of bacterial genomes & plasmids | 12/9/2020 | | detailed information |
bam2fastx | 1.3.0 | Linux | Conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data | 8/6/2019 | | detailed information |
bamtools | 2.5.1 | Linux | BAM file processing and filtering. | 12/13/2011 | 2/27/2018 | detailed information |
bamUtil | 1.0.14 | Linux | bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. | 1/17/2019 | | detailed information |
BarNone | 1.0 | Linux | Matching and counting sequencing barcodes (e.g., from Bar-Seq) to a catalog. Inexact matching via minimum Levenshtein distance. | 1/13/2020 | | detailed information |
Basset | 0.1.0 | Linux | Deep convolutional neural networks for DNA sequence analysis. | 5/15/2017 | | detailed information |
BayeScan | 2.1 | Linux | BayeScan 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 | 1.1 | Linux | BayeScEnv 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 |
baypass | 2.2 | Linux | population 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 |
BBmap | 38.86 | Linux | This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. | 11/6/2015 | 7/30/2020 | detailed information |
BCFtools | 1.11 | Linux | bcftools — utilities for variant calling and manipulating VCFs and BCFs. | 2/20/2017 | 10/28/2020 | detailed information |
bcl2fastq | 2.20.0 | Linux | bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. | 8/7/2017 | 11/14/2017 | detailed information |
BCP | 1.1 | Linux | Bayesian Change-point Model (BCP) is a method for analysis different type of ChIP-seq data. | 10/23/2017 | | detailed information |
Beagle | 5.0 | Linux | Phasing, imputation, Haplotype inferrance | 11/18/2013 | 1/2/2019 | detailed information |
Beast2 | 2.5.2 | Linux | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. | 3/27/2017 | 2/15/2019 | detailed information |
bedops | 2.4.35 | Linux | Fast BED file operaion. | 7/26/2013 | 4/25/2019 | detailed information |
BEDtools | 2.29.2 | Linux | BED file operation. | 2/6/2012 | 1/14/2020 | detailed information |
bfc | 20150417 | Linux | High-performance error correction for Illumina resequencing data | 10/18/2016 | | detailed information |
bgc | 1.01 | Linux | bgc implements Bayesian estimation of genomic clines to quantify introgression at many loci. | 2/12/2013 | 2/12/2013 | detailed information |
bgen | 20180807 | Linux | BGEN: a binary file format for imputed genotype and haplotype data | 11/30/2018 | | detailed information |
bigQF | 1.3-1 | Linux | R package for large quadratic forms | 2/26/2018 | | detailed information |
bigWig | 20171211 | Linux | R library to work with UCSC bigwig files | 12/11/2017 | | detailed information |
bioawk | 20180714 | Linux | Bioawk is an extension to Brian Kernighan's awk | 7/24/2018 | | detailed information |
biobambam | 0.0.125 | Linux | This package contains tools for processing BAM files. | 2/28/2014 | 2/28/2014 | detailed information |
Bioconductor | 3.0 | Linux | R package for genomics data analysis. | 7/19/2013 | 3/24/2014 | detailed information |
biom-format | 20180521 | Linux | The 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 |
BioPerl | 1.6.922 | Linux | PERL library for general bioinformatics. | 12/13/2011 | 3/24/2014 | detailed information |
BioPython | 1.60 | Linux | | 2/27/2012 | 1/31/2013 | detailed information |
Birdsuite | 1.5.5 | Linux | Set 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 |
Bismark | 0.16.1 | Linux | A bisulfite read mapper and methylation caller | 11/20/2012 | 6/30/2016 | detailed information |
blasr | 20180816 | Linux | The PacBio long read aligner | 9/24/2014 | 8/16/2018 | detailed information |
BLAST | 2.9.0 | Linux | Sequence alignment. | 12/13/2011 | 4/25/2019 | detailed information |
BLAST_to_BED | 20200928 | Linux | Parses a BLAST XML file and creates a BED file | 9/28/2020 | | detailed information |
blast2go | DB: March.2020: Software: v1.4.4 | Linux | Gene Ontology annotation and function enrichment analysis. | 4/15/2013 | 5/4/2020 | detailed information |
BLAT | 34 | Linux | Sequence alignment. | 12/13/2011 | 5/1/2012 | detailed information |
BLUPF90 | 2019.04.23 | Linux | Fortran 90/95 software for mixed model computations in animal breeding | 5/8/2019 | | detailed information |
BMGE | 1.12 | Linux | Selection of phylogenetic informative regions from multiple sequence alignments | 3/9/2018 | | detailed information |
bmtagger | 2/21/14 | Linux | Best Match Tagger for removing human reads from metagenomics datasets | 10/6/2016 | | detailed information |
Boost | 1.62.0 | Linux | Boost provides free peer-reviewed portable C++ source libraries. | 12/17/2014 | 10/25/2017 | detailed information |
Bowtie | 1.1.2 | Linux | An ultrafast, memory-efficient short read aligner. | 12/13/2011 | 3/22/2016 | detailed information |
Bowtie2 | 2.3.5.1 | Linux | An ultrafast, memory-efficient short read aligner. | 5/1/2012 | 4/25/2019 | detailed information |
BPGA | 1.3 | Linux | Comprehensive pan genome analysis of microorganisms | 10/25/2017 | | detailed information |
Bracken | 2.0 | Linux | A companion program to Kraken 1.0 or Kraken 2.0. | 2/12/2019 | | detailed information |
BRAKER | 2.1.5 | Linux | Uses genomic and RNA-Seq data to automatically generate full gene structure annotations in novel genome | 9/1/2019 | 7/12/2020 | detailed information |
BRAT-NextGen | 20150505 | Linux | NextGen software for Bayesian analysis of recombinations in whole-genome DNA sequence data, | 2/27/2019 | | detailed information |
BreedingSchemeLanguage | 20180424 | Linux | We present here a simple and flexible simulation platform, the breeding scheme language (BSL) | 4/24/2018 | | detailed information |
breseq | 0.32.1 | Linux | breseq 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. | 6/29/2016 | 7/9/2018 | detailed information |
brocc | 1.4.0 | Linux | Generate consensus-based taxonomic assignments from BLAST results. | 1/4/2019 | | detailed information |
BSseeker2 | 2.1.0 | Linux | Mapping the bisulfite-treated short reads | 1/23/2017 | | detailed information |
BUSCO | 4.1.4 | Linux | Assessing genome assembly and annotation completeness. | 1/22/2016 | 7/15/2020 | detailed information |
BWA | 0.7.17 | Linux | BWA is a software package for mapping low-divergent sequences against a large reference genome. | 12/13/2011 | 4/25/2019 | detailed information |
bwa-meth | v0.2.0 | Linux | aligners for BS-Seq | 1/17/2018 | | detailed information |
cactus | 1.2.3 | Linux | Cactus is a reference-free whole-genome multiple alignment program | 10/9/2018 | 10/26/2020 | detailed information |
CAFE | 4.2.1 | Linux | Analysis of gene Family Evolution | 12/3/2019 | | detailed information |
canu | 2.1.1 | Linux | assemble pacbio or nanopore reads | 2/11/2016 | 12/12/2020 | detailed information |
CAP3 | 12/21/07 | Linux | A DNA Sequence Assembly Program | 4/4/2014 | | detailed information |
CarveMe | 8_28_2019 | Linux | Constructs 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. | 8/28/2019 | | detailed information |
cBar | 1.2 | Linux | Distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data | 11/1/2017 | | detailed information |
CBSU RNAseq | 1.0 | Linux | | 12/13/2011 | 5/1/2012 | detailed information |
CCTpack | 20181009 | Linux | Consensus analysis, model-based clustering, and cultural consensus theory applications to response data (e.g. questionnaires). | 10/9/2018 | | detailed information |
cd-hit | 4.8.1 | Linux | cluster reads based on sequence similarity | 9/28/2015 | 7/21/2020 | detailed information |
cdbfasta | 20191012 | Linux | Indexing and retrieval tools for FASTA files | 10/13/2019 | | detailed information |
CEGMA | 2.5 | Linux | CEGMA (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 |
CellRanger | 6.0.0 | Linux | A set of analysis pipelines that perform sample demultiplexing, barcode processing, and single cell 3’ gene counting. | 5/15/2017 | 3/31/2021 | detailed information |
cellranger-arc | 1.0.1 | Linux | A 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-atac | 1.2.0 | Linux | Set of analysis pipelines that process Chromium Single Cell ATAC data | 4/1/2019 | 11/27/2019 | detailed information |
cellranger-dna | 1.1.0 | Linux | et of analysis pipelines that process Chromium single cell DNA sequencing output | 3/8/2020 | 3/8/2020 | detailed information |
centrifuge | 20171218 | Linux | Microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers. | 12/18/2017 | | detailed information |
centroFlye | 20200709 | Linux | Centromere assembly using long error-prone reads | 7/9/2020 | | detailed information |
CFM-ID | 2 | Linux | Processing of EI-MS (GC-MS) and ESI-MS/MS (LC-MS) data for identification of metabolites. | 10/18/2019 | | detailed information |
CFSAN SNP pipeline | 2.2.1 | Linux | SNP 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. | 2/6/2018 | 3/30/2021 | detailed information |
CheckM | 1.1.2 | Linux | CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes | 10/11/2016 | 4/1/2020 | detailed information |
chimera | 1.13.1 | Linux | Interactive visualization and analysis of molecular structures and related data. | 3/17/2019 | | detailed information |
chromosomer | chromosomer | Linux | Chromosomer is a reference-assisted assembly tool for producing draft chromosome sequences. | 6/18/2018 | | detailed information |
Circlator | 1.5.5 | Linux | A tool to circularize genome assemblies | 4/8/2018 | | detailed information |
Circos | 0.67-7 | Linux | Circos is a software package for visualizing data and information. | 3/24/2015 | | detailed information |
Circuitscape | 4.0.5 | Linux | An open-source program that uses circuit theory to model connectivity in heterogeneous landscapes | 4/16/2015 | | detailed information |
CITE-seq-Count | 1.4.3 | Linux | Count antibody TAGS from a CITE-seq and/or cell hashing experiment. | 5/14/2020 | | detailed information |
clues | 20201201 | Linux | Inferring selection and allele frequency trajectories from DNA sequence data | 12/1/2020 | | detailed information |
CLUMPP | 1.1.2 | Linux | CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. | 4/10/2017 | | detailed information |
clust | 1.10.8 | Linux | Optimised consensus clustering of one or more heterogeneous datasets. | 11/27/2019 | | detailed information |
Clustal Omega | 1.2.4 | Linux | Multiple sequence alignment | 2/24/2015 | 4/25/2019 | detailed information |
CLUSTALW | 2.1 | Linux | General purpose DNA or protein multiple sequence alignment program for three or more sequences. | 12/13/2011 | 5/1/2012 | detailed information |
Cluster | 1.52 | Linux | The open source clustering software implementing the most commonly used clustering methods for gene expression data analysis. | 4/28/2014 | | detailed information |
cmake | 3.6.3 | Linux | CMake is an open-source, cross-platform family of tools designed to build, test and package software | 5/22/2017 | | detailed information |
CNVnator | 0.3 | Linux | A tool for CNV discovery and genotyping from depth of read mapping | 6/23/2015 | 6/23/2015 | detailed information |
compat | 0.8 | Linux | The 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 trees | 4/5/2018 | | detailed information |
CONCOCT | 1.1.0 | Linux | A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. | 3/20/2018 | 11/1/2019 | detailed information |
Conda | 20181201 | Linux | An open source package management system and environment management system. | 12/2/2018 | | detailed information |
copyNumberDiff | 20200708 | Linux | compare two groups of individuals to see if there are copy number differences the correlate with group assignment. | 5/21/2018 | 7/8/2020 | detailed information |
cortex_var | 1.0.5.21 | Linux | cortex_var is a tool for genome assembly and variation analysis from sequence data. | 7/18/2017 | | detailed information |
CRISPRCasFinder | 20181004 | Linux | The CRISPRCasFinder program enables the easy detection of CRISPRs and cas genes in user-submitted sequence data | 10/4/2018 | | detailed information |
CRISPResso | 1.0.13 | Linux | CRISPResso is a software pipeline for the analysis of targeted CRISPR-Cas9 sequencing data. | 11/12/2018 | | detailed information |
CrossMap | 0.3.8 | Linux | CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies. | 5/11/2016 | 7/21/2020 | detailed information |
CRT | | Linux | CRISPR Recognition Tool | 3/24/2017 | | detailed information |
cuda | 8.0.61 | Linux | A parallel computing platform and programming model invented by NVIDIA. | 5/15/2017 | | detailed information |
Cufflinks | 2.2.1 | Linux | RNA-seq reference guided transcript assembly, quantification and differential expressed gene identification | 12/13/2011 | 5/6/2014 | detailed information |
cutadapt | 2.1 | Linux | cutadapt removes adapter sequences from high-throughput sequencing data. | 10/11/2013 | 8/1/2019 | detailed information |
dadi | 2.1.0 | Linux | It implements a method for demographic inference from genetic data, based on a diffusion approximation to the allele frequency spectrum. | 5/12/2015 | 8/11/2020 | detailed information |
dadi-1.6.3_modif | 1.6.3_mod | Linux | Modified Dadi software | 6/7/2017 | | detailed information |
danpos | 2.2.2 | Linux | A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing | 7/21/2019 | | detailed information |
dDocent | 2.2.16 | Linux | simple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing. | 8/29/2017 | | detailed information |
DeconSeq | 0.4.3 | Linux | DECONtamination of SEQuence data using a modified version of BWA-SW | 11/6/2015 | | detailed information |
Deepbinner | 0.2.0 | Linux | Demultiplexing barcoded Oxford Nanopore sequencing reads. | 11/25/2019 | | detailed information |
DeepTE | 20200521 | Linux | Classify transposons with unknown classification via Convolutional Neural Network. | 5/21/2020 | | detailed information |
deepTools | 3.5.0 | Linux | A suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data. | 10/14/2016 | 12/2/2020 | detailed information |
defusion | 20180531 | Linux | A tool to entangle MAKER fused genome annotation | 5/31/2018 | | detailed information |
delly | 0.8.7 | Linux | DELLY 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. | 11/13/2013 | 1/21/2021 | detailed information |
DESMAN | 2.1 | Linux | De novo Extraction of Strains from MetAgeNomes | 8/13/2019 | | detailed information |
destruct | 1.1 | Linux | distruct 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 |
DETONATE | 1.10 | Linux | Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies | 2/16/2016 | | detailed information |
diamond | 2.0.4 | Linux | Accelerated BLAST compatible local sequence aligner | 11/24/2014 | 10/1/2020 | detailed information |
diploSHIC | 20210402 | Linux | diploS/HIC uses a deep convolutional neural network to identify hard and soft selective sweep in population genomic data. | 10/29/2018 | 4/2/2021 | detailed information |
discoal | 0.1.4 | Linux | discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples | 7/11/2019 | | detailed information |
Discovar | 52488 | Linux | DISCOVAR is a small genome assembler and variant caller from Broad Institute. Uses 250pb PE PCR-free Illumina reads. | 8/11/2014 | 2/12/2016 | detailed information |
Discovar de novo | 52488 | Linux | Experimental de novo assembler for large genomes using 250pb PE PCR-free Illumina reads. From Broad Institute. | 8/11/2014 | 2/12/2016 | detailed information |
distruct | 1.1 | Linux | distruct 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 |
DiTASiC | 0.2 | Linux | Abundance estimation and differential abundance assessment of individual taxa in metagenomics samples | 3/7/2019 | | detailed information |
DIYABC | 2.1.0 | Linux | a user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers | 10/22/2018 | | detailed information |
Docker | 1.12.5 | Linux | Executes applications in containers that are isolated from main operating system (OS-level virtualization) | 2/14/2017 | | detailed information |
dREG | 20200515 | Linux | Detection of Regulatory DNA Sequences using GRO-seq Data. | 4/28/2016 | 5/15/2020 | detailed information |
dREG.HD | 20180601 | Linux | The dREG package uses support vector regression (SVR) to identify active TREs solely from PRO-seq data. | 12/12/2017 | 6/1/2018 | detailed information |
drep | 2.3.2 | Linux | Rapidly comparing large numbers of genomes. | 10/29/2019 | | detailed information |
drive | 0.3.9 | Linux | google drive client | 8/21/2020 | | detailed information |
Drop-seq | 1.12 | Linux | Drop-seq is a technology that allows biologists to analyze genome-wide gene expression in thousands of individual cells in a single experiment. | 6/11/2017 | | detailed information |
dropEst | 0.8.5 | Linux | Pipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements. | 1/16/2019 | | detailed information |
dropSeqPipe | 20171014 | Linux | his pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab. | 6/16/2017 | 10/14/2017 | detailed information |
dsk | 1.6706 | Linux | DSK is a k-mer counting software, similar to Jellyfish. | 10/17/2014 | | detailed information |
dssat | 4.7 | Linux | DSSAT Cropping System Model | 2/5/2021 | | detailed information |
Dsuite | 20190611 | Linux | Fast calculation of the ABBA-BABA statistics across many populations/species | 6/11/2019 | | detailed information |
dTOX | 20190928 | Linux | Motif-based discriminative method to predict transcription factor binding from PRO-seq, ATAC-seq, or DNase-I-seq data | 1/10/2020 | | detailed information |
duphold | 0.2.1 | Linux | uphold your DUP and DEL calls | 5/15/2020 | | detailed information |
dynare | 4.5.7 | Linux | A software platform for handling a wide class of economic models | 2/18/2020 | | detailed information |
ea-utils | rev822 | Linux | Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. | 3/10/2015 | | detailed information |
ecopcr | 0.5.0 | Linux | DNA barcoding is a tool for characterizing the species origin using a short sequence | 9/3/2015 | | detailed information |
ecoPrimers | 0.5 | Linux | Finds primers from a set of sequences | 2/5/2019 | | detailed information |
ectyper | v0.8.1 | Linux | cyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats. | 8/28/2018 | 3/21/2019 | detailed information |
EDGE | 1.1 | Linux | Next Generation Sequencing pipeline | 6/8/2016 | | detailed information |
edirect | 9.10 | Linux | Access to the NCBI's suite of interconnected databases | 6/22/2018 | | detailed information |
eems | 20181127 | Linux | analyzing and visualizing spatial population structure from geo-referenced genetic samples. | 11/27/2018 | | detailed information |
EgaCryptor | | Linux | EgaCryptor is a JAVA based client, which enables submitters to produce EGA compliant files by encrypting each file to be submitted and generating the encrypted and unencrypted md5sum for each file. | 1/13/2020 | | detailed information |
EGAD | 08092019 | Linux | calculate functional properties of networks based on guilt by association methods. | 8/9/2019 | | detailed information |
EIGENSOFT | 7.2.1 | Linux | The EIGENSOFT package combines functionality from population genetics methods (Patterson et al. 2006) and EIGENSTRAT stratification correction method (Price et al. 2006). | 10/14/2013 | 8/19/2019 | detailed information |
EMBOSS | 6.6.0 | Linux | European Molecular Biology Open Software Suite | 11/6/2013 | 11/6/2013 | detailed information |
Empress | 0.1.dev0 | Linux | Fast and scalable phylogenetic tree viewer (QIIME 2 plugin) | 3/26/2020 | 4/21/2020 | detailed information |
entropy | | Linux | admixture proportion and admixture class models | 9/9/2017 | | detailed information |
epa-ng | 0.3.8 | Linux | Evolutionary Placement Algorithm (EPA) | 9/27/2020 | | detailed information |
ephem | 3.7.6.0 | Linux | Python package for performing high-precision astronomy computations | 12/26/2017 | | detailed information |
epic2 | 20190416 | Linux | An ultraperformant reimplementation of SICER | 4/16/2019 | | detailed information |
ermineJ | 3.0.2 | Linux | ErmineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. A typical goal is to determine whether particular biological pathways are "doing something interesting" in an experiment that generates long lists of candidates. | 9/22/2016 | | detailed information |
ete3 | 3.1.1 | Linux | A Python framework for the analysis and visualization of trees. | 10/4/2017 | 3/1/2020 | detailed information |
EVM | 1.1.1 | Linux | EVidenceModeler | 10/17/2020 | | detailed information |
exabayes | 1.4.1 | Linux | ExaBayes is a software package for Bayesian tree inference. | 2/16/2016 | 2/16/2016 | detailed information |
exonerate | 2.2.0 | Linux | exonerate is a generic tool for pairwise sequence comparison | 1/23/2013 | 1/23/2013 | detailed information |
ExpansionHunterDenovo-v0.8.0 | 0.8.0 | Linux | Detection novel expansions of short tandem repeats (STRs). | 12/4/2019 | | detailed information |