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BioHPC Cloud:
: Software

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NameVersionOSAboutInstalledUpdatedMore
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
ABRicatev0.8LinuxMass screening of contigs for antimicrobial resistance or virulence genes. 6/11/2018 detailed information
ABruijn20161221LinuxABruijn is a de novo assembler for PacBio and Oxford Nanopore Technologies reads. 12/21/2016 detailed information
ABySS 1.9.0LinuxIllumina short reads assembly tool.12/13/20115/9/2016detailed 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
Admixture1.23LinuxSoftware tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.2/19/20142/19/2014detailed 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
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
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
AMRFinder3.6.15LinuxNCBI Antimicrobial Resistance Gene Finder4/8/2020 detailed information
analysis0.8.4Linux C++ software for evolutionary genetic analysis.9/2/2014 detailed information
ANGSD0.931-4-g10d2f2bLinuxANGSD 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.3/27/201510/2/2019detailed information
Annovar20130823LinuxSNP/INDEL annotation.12/13/20111/22/2015detailed 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
anvio6.2LinuxIntegrated multi-omics at scale7/30/2020 detailed information
apollo20170925LinuxManual genome annotation9/25/2017 detailed information
arcs1.1.1LinuxScaffold genome sequence assemblies using linked read sequencing data6/11/2020 detailed information
Arlequin3.5.2.2LinuxAn Integrated Software for Population Genetics Data Analysis10/31/2017 detailed information
aspera3.9.9LinuxIBM Aspera Connect is an install-on-demand application that facilitates high-speed uploads and downloads with an Aspera transfer server.10/12/20183/13/2020detailed information
assembly-stats1.0.1LinuxGet assembly statistics from FASTA and FASTQ files.4/14/2019 detailed information
atac-seq-pipeline1.7.0LinuxThis pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data. 10/27/20184/6/2020detailed 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
ATSAS 2.5.0-2LinuxA program suite for small-angle scattering data analysis from biological macromolecules.12/13/20111/31/2013detailed information
Augustus3.3.3LinuxAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences1/23/201310/13/2019detailed information
AWS command line interface1.14.39LinuxProvides command-line access to Amazon Web Services2/15/2018 detailed information
axe0.3.2LinuxRapid competitive read demulitplexer. 3/5/2018 detailed information
BactSNP1.1.0LinuxBactSNP is a tool to identify SNPs among bacterial isolates. 6/13/2019 detailed information
bam2fastx1.3.0LinuxConversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data8/6/2019 detailed information
bamtools2.5.1LinuxBAM file processing and filtering.12/13/20112/27/2018detailed information
bamUtil1.0.14LinuxbamUtil is a repository that contains several programs that perform operations on SAM/BAM files.1/17/2019 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
BBmap38.86LinuxThis package includes BBMap, a short read aligner, as well as various other bioinformatic tools.11/6/20157/30/2020detailed information
BCFtools1.9Linuxbcftools — utilities for variant calling and manipulating VCFs and BCFs.2/20/20174/25/2019detailed 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
Beast22.5.2LinuxBEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.3/27/20172/15/2019detailed 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
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
BioPerl1.6.922LinuxPERL library for general bioinformatics.12/13/20113/24/2014detailed 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
Bismark0.16.1LinuxA bisulfite read mapper and methylation caller 11/20/20126/30/2016detailed information
blasr20180816LinuxThe PacBio long read aligner9/24/20148/16/2018detailed information
BLAST2.9.0LinuxSequence alignment.12/13/20114/25/2019detailed information
blast2goDB: March.2020: Software: v1.4.4LinuxGene Ontology annotation and function enrichment analysis.4/15/20135/4/2020detailed information
BLAT34LinuxSequence alignment.12/13/20115/1/2012detailed 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
Boost1.62.0LinuxBoost provides free peer-reviewed portable C++ source libraries.12/17/201410/25/2017detailed information
Bowtie1.1.2LinuxAn ultrafast, memory-efficient short read aligner.12/13/20113/22/2016detailed information
Bowtie22.3.5.1LinuxAn ultrafast, memory-efficient short read aligner.5/1/20124/25/2019detailed information
BPGA1.3LinuxComprehensive pan genome analysis of microorganisms10/25/2017 detailed information
Bracken2.0LinuxA companion program to Kraken 1.0 or Kraken 2.0.2/12/2019 detailed information
BRAKER2.1.5LinuxUses genomic and RNA-Seq data to automatically generate full gene structure annotations in novel genome9/1/20197/12/2020detailed information
BRAT-NextGen20150505LinuxNextGen software for Bayesian analysis of recombinations in whole-genome DNA sequence data,2/27/2019 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
BSseeker22.1.0LinuxMapping the bisulfite-treated short reads1/23/2017 detailed information
BUSCO4.0.6LinuxAssessing genome assembly and annotation completeness.1/22/20167/15/2020detailed 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-methv0.2.0Linuxaligners for BS-Seq1/17/2018 detailed information
cactus20181009LinuxCactus is a reference-free whole-genome multiple alignment program10/9/2018 detailed information
CAFE4.2.1LinuxAnalysis of gene Family Evolution12/3/2019 detailed information
canu2.0Linuxassemble pacbio or nanopore reads2/11/20167/27/2020detailed information
CAP312/21/07LinuxA DNA Sequence Assembly Program4/4/2014 detailed information
CarveMe8_28_2019LinuxConstructs 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
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
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
CellRanger3.1.0LinuxA set of analysis pipelines that perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.5/15/20177/29/2019detailed information
cellranger-atac1.2.0LinuxSet of analysis pipelines that process Chromium Single Cell ATAC data4/1/201911/27/2019detailed 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 pipeline2.0.2LinuxSNP 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. 2/6/201810/9/2018detailed information
CheckM1.1.2LinuxCheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes10/11/20164/1/2020detailed information
chimera1.13.1LinuxInteractive visualization and analysis of molecular structures and related data.3/17/2019 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-Count1.4.3LinuxCount antibody TAGS from a CITE-seq and/or cell hashing experiment.5/14/2020 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
clust1.10.8LinuxOptimised consensus clustering of one or more heterogeneous datasets.11/27/2019 detailed 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
cmake3.6.3LinuxCMake is an open-source, cross-platform family of tools designed to build, test and package software5/22/2017 detailed information
CNVnator0.3LinuxA tool for CNV discovery and genotyping from depth of read mapping6/23/20156/23/2015detailed 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
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
CRISPRCasFinder20181004LinuxThe CRISPRCasFinder program enables the easy detection of CRISPRs and cas genes in user-submitted sequence data10/4/2018 detailed information
CRISPResso1.0.13LinuxCRISPResso is a software pipeline for the analysis of targeted CRISPR-Cas9 sequencing data.11/12/2018 detailed information
CrossMap0.3.8LinuxCrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies.5/11/20167/21/2020detailed 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
cutadapt2.4Linuxcutadapt removes adapter sequences from high-throughput sequencing data.10/11/20138/1/2019detailed information
dadi2.0.5LinuxIt implements a method for demographic inference from genetic data, based on a diffusion approximation to the allele frequency spectrum.5/12/20157/7/2020detailed 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
dDocent2.2.16Linuxsimple bash wrapper to QC, assemble, map, and call SNPs from almost any kind of RAD sequencing.8/29/2017 detailed 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
deepTools3.3.0LinuxA suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data.10/14/20167/10/2019detailed information
defusion20180531LinuxA tool to entangle MAKER fused genome annotation5/31/2018 detailed information
delly0.8.3LinuxDELLY 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. 11/13/20135/13/2020detailed 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
diamond0.9.34LinuxAccelerated BLAST compatible local sequence aligner11/24/20146/8/2020detailed information
diploSHIC20181029LinuxdiploS/HIC uses a deep convolutional neural network to identify hard and soft selective sweep in population genomic data.10/29/2018 detailed 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
distruct1.1Linuxdistruct 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
DiTASiC0.2LinuxAbundance estimation and differential abundance assessment of individual taxa in metagenomics samples3/7/2019 detailed information
DIYABC2.1.0Linuxa user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers10/22/2018 detailed information
Docker1.12.5LinuxExecutes applications in containers that are isolated from main operating system (OS-level virtualization)2/14/2017 detailed information
dREG20200515LinuxDetection of Regulatory DNA Sequences using GRO-seq Data.4/28/20165/15/2020detailed information
dREG.HD20180601LinuxThe dREG package uses support vector regression (SVR) to identify active TREs solely from PRO-seq data.12/12/20176/1/2018detailed information
drep2.3.2LinuxRapidly comparing large numbers of genomes. 10/29/2019 detailed information
Drop-seq1.12LinuxDrop-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
dropEst0.8.5LinuxPipeline for estimating molecular count matrices for droplet-based single-cell RNA-seq measurements. 1/16/2019 detailed information
dropSeqPipe20171014Linuxhis pipeline is based on snakemake and the dropseq tools provided by the McCarroll Lab.6/16/201710/14/2017detailed information
dsk1.6706LinuxDSK is a k-mer counting software, similar to Jellyfish.10/17/2014 detailed information
Dsuite20190611LinuxFast calculation of the ABBA-BABA statistics across many populations/species6/11/2019 detailed information
dTOX20190928LinuxMotif-based discriminative method to predict transcription factor binding from PRO-seq, ATAC-seq, or DNase-I-seq data1/10/2020 detailed information
duphold0.2.1Linuxuphold your DUP and DEL calls5/15/2020 detailed information
dynare4.5.7LinuxA software platform for handling a wide class of economic models2/18/2020 detailed information
ea-utilsrev822LinuxCommand-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc.3/10/2015 detailed information
ecopcr0.5.0LinuxDNA barcoding is a tool for characterizing the species origin using a short sequence9/3/2015 detailed information
ecoPrimers0.5Linux Finds primers from a set of sequences 2/5/2019 detailed information
ectyper v0.8.1Linuxcyper is a standalone serotyping module for Escherichia coli. It supports fasta and fastq file formats.8/28/20183/21/2019detailed information
EDGE1.1LinuxNext Generation Sequencing pipeline6/8/2016 detailed information
edirect9.10LinuxAccess to the NCBI's suite of interconnected databases 6/22/2018 detailed information
eems20181127Linuxanalyzing and visualizing spatial population structure from geo-referenced genetic samples.11/27/2018 detailed information
EgaCryptor LinuxEgaCryptor 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
EGAD08092019Linuxcalculate functional properties of networks based on guilt by association methods.8/9/2019 detailed information
EIGENSOFT7.2.1LinuxThe EIGENSOFT package combines functionality from population genetics methods (Patterson et al. 2006) and EIGENSTRAT stratification correction method (Price et al. 2006).10/14/20138/19/2019detailed information
EMBOSS6.6.0LinuxEuropean Molecular Biology Open Software Suite11/6/201311/6/2013detailed information
Empress0.1.dev0LinuxFast and scalable phylogenetic tree viewer (QIIME 2 plugin)3/26/20204/21/2020detailed information
entropy Linuxadmixture proportion and admixture class models9/9/2017 detailed information
ephem3.7.6.0LinuxPython package for performing high-precision astronomy computations12/26/2017 detailed information
epic220190416LinuxAn ultraperformant reimplementation of SICER4/16/2019 detailed information
ermineJ3.0.2LinuxErmineJ 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
ete33.1.1LinuxA Python framework for the analysis and visualization of trees.10/4/20173/1/2020detailed information
exabayes1.4.1LinuxExaBayes is a software package for Bayesian tree inference. 2/16/20162/16/2016detailed information
exonerate2.2.0Linuxexonerate is a generic tool for pairwise sequence comparison1/23/20131/23/2013detailed information
ExpansionHunterDenovo-v0.8.00.8.0LinuxDetection novel expansions of short tandem repeats (STRs).12/4/2019 detailed information
eXpress1.5.1LinuxA streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences9/25/2014 detailed information
FALCON20160919LinuxFalcon Genome Assembly Tool Kit (PacBio)4/28/20169/19/2016detailed information
FALCON_unzip20160919LinuxFor Phased Diploid Genome Assembly with PacBio reads.9/19/2016 detailed information
Fast-GBS20170110Linux Extract a high-quality SNP catalog starting from FASTQ files obtained from sequencing genotyping-by-sequencing (GBS) libraries.1/23/2017 detailed information
fasta36.3.8dLinuxSequence search and alignment including global alignment.2/7/2017 detailed information
FastANI1.3LinuxFast alignment-free computation of whole-genome Average Nucleotide Identity (ANI)3/7/20192/14/2020detailed information
fastcluster20170926LinuxThis library provides Python functions for hierarchical clustering.9/26/2017 detailed information
FastME2.1.6.1LinuxFastME provides distance algorithms to infer phylogenies.1/18/2019 detailed information
FastML20150324LinuxMaximum Likelihood ancestral sequence reconstruction3/24/2015 detailed information
fastp0.20.0LinuxA tool designed to provide fast all-in-one preprocessing for FastQ files12/14/20172/7/2020detailed information
FastQ Screen0.14.0LinuxScreen a library of sequences in FastQ format against a set of sequence databases8/12/2019 detailed information
fastq_pair1.0LinuxRewrite paired end fastq files to make sure that all reads have a mate and to separate out singletons.3/19/2019 detailed information
fastq_species_detector1LinuxBLAST a sample of eads form a fastq file agains nt database and determine fractions of reads with best matches to different speices7/17/2014 detailed information
FastQC0.11.8LinuxA quality control tool for high throughput sequence data.4/16/20134/25/2019detailed information
fastsimcoal262.6.0.2Linuxhttp://cmpg.unibe.ch/software/fastsimcoal2/8/28/2018 detailed information

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