Name | Version | OS | About | Installed | Updated | More |
3D Slicer | 5.6.0 | Linux | Analyzing and understanding medical image data | 11/29/2023 | | detailed information |
3d-dna | 08012019 | Linux | 3D de novo assembly (3D-DNA) pipeline | 4/21/2021 | | detailed information |
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 | v1.0.0 | Linux | Mass screening of contigs for antimicrobial resistance or virulence genes. | 6/11/2018 | 2/16/2023 | 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 |
AF_unmasked | 20231025 | Linux | AlphaFold unmasked to integrate experiments and predictions | 10/25/2023 | | detailed information |
AFProfile | 20230713 | Linux | Protein complex prediction with AlphaFold-multimer by denoising the MSA profile. | 8/30/2023 | | detailed information |
AGAT | 1.2.0 | Linux | Another Gtf/Gff Analysis Toolkit | 1/24/2024 | | 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 |
AliTV-Perl interface | 1.0.6 | Linux | AliTV-Perl interface | 11/29/2022 | | 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 |
Alphafold | 2.3.2 | Linux | Protein structure prediction. | 7/27/2021 | 7/8/2023 | detailed information |
Alphafold3 | alphafold3 | Linux | Protein structure prediction | 12/2/2024 | | detailed information |
alphapickle | 1.4.1 | Linux | producing plots and user-legible files from the output of AlphaFold2 | 3/26/2024 | | detailed information |
Alphapulldown | 2.0.0b5 | Linux | Protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer | 3/24/2024 | 8/30/2024 | detailed information |
AlphScore | 0.9 | Linux | Predicting the pathogenicity of missense variants using features derived from AlphaFold2 | 6/13/2024 | | 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 | 3.12.8 | Linux | NCBI Antimicrobial Resistance Gene Finder | 4/8/2020 | 5/28/2024 | detailed information |
analysis | 0.8.4 | Linux | C++ software for evolutionary genetic analysis. | 9/2/2014 | | detailed information |
ANGSD | 0.940 | 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 | 10/20/2022 | detailed information |
AnnotaPipeline | 20231210 | Linux | Gene function annotation | 12/10/2023 | | detailed information |
Annovar | 20130823 | Linux | SNP/INDEL annotation. | 12/13/2011 | 1/22/2015 | detailed information |
ant | 1.9.9 | Linux | Apache 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 |
antiSMASH | 7.1 | 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 | 6/13/2024 | detailed information |
anvio | 8.0 | Linux | Integrated multi-omics at scale | 7/30/2020 | 10/30/2023 | 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 |
aria2 | 1.36.0 | Linux | Fast download utility | 7/4/2023 | | detailed information |
ariba | 2.14.6 | Linux | Antimicrobial Resistance Identification By Assembly | 2/8/2023 | | 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 |
ASEQ | 1.1.11 | Linux | Fast allele-specific studies from next-generation sequencing data | 5/4/2023 | | detailed information |
aspera | 4.2.3.197 | 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 | 12/7/2022 | detailed information |
assembly-stats | 1.0.1 | Linux | Get assembly statistics from FASTA and FASTQ files. | 4/14/2019 | | detailed information |
ASTRAL | 5.7.8 | Linux | Estimating an unrooted species tree given a set of unrooted gene trees. | 2/2/2021 | | detailed information |
atac-seq-pipeline | 2.2.2 | Linux | This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data. | 10/27/2018 | 12/5/2023 | 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 | 3.4.0 | Linux | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences | 1/23/2013 | 1/2/2022 | 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 |
axel | 2.17.10 | Linux | accelerate the download process by using multiple connections per file | 6/3/2021 | | detailed information |
BA3 | 3.0.5.6 | Linux | BayesAss edition 3 | 11/17/2023 | | detailed information |
BactSNP | 1.1.0 | Linux | BactSNP is a tool to identify SNPs among bacterial isolates. | 6/13/2019 | | detailed information |
bakta | 1.9.3 | Linux | Annotation of bacterial genomes & plasmids | 12/9/2020 | 5/8/2024 | detailed information |
bamsnap | 0.2.19 | Linux | Visualization tool for sequencing reads in BAM files | 1/5/2024 | | detailed information |
bamsurgeon | 1.4.1 | Linux | Adding genomic variants to SAM/BAM/CRAM files, used for testing variant callers | 1/17/2023 | | detailed information |
bamtools | 2.5.2 | Linux | BAM file processing and filtering. | 12/13/2011 | 9/5/2023 | 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 |
barcode_splitter | 0.18.6 | Linux | A utility to split multiple sequence files using multiple sets of barcodes. | 4/12/2022 | | 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 |
bayesR | 20210104 | Linux | Bayesian hierarchical model for complex trait analysis | 9/18/2023 | | detailed information |
baypass | 2.4.1 | 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 | 5/19/2024 | detailed information |
bazel | 5.1.0 | Linux | Build and test software | 3/28/2022 | | detailed information |
BBMap/BBTools | 39.10 | Linux | The BBTools package includes BBMap, a short read aligner, and various other useful bioinformatic tools | 11/6/2015 | 10/1/2024 | detailed information |
BCFtools | 1.20 | Linux | bcftools — utilities for variant calling and manipulating VCFs and BCFs. | 2/20/2017 | 5/23/2024 | detailed information |
BCL convert | 4.2.7-2 | Linux | Convert, demultiplex Illumina BCL files into fastq | 4/17/2024 | | 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 |
bdbag | 1.7.3 | Linux | command line tools for bdbag | 8/29/2024 | | detailed information |
Beagle | 5.4 | Linux | Phasing, imputation, Haplotype inferrance | 11/18/2013 | 10/9/2024 | detailed information |
beagle-lib | 4.0.1 | Linux | beagle library used by beast2 et al | 10/9/2024 | | detailed information |
BEAST | 1.10.4 | Linux | Bayesian analysis of molecular sequences using MCMC. | 10/8/2024 | | detailed information |
BEAST X | 10.5.0 | Linux | Bayesian analysis of molecular sequences using MCMC. | 10/9/2024 | | detailed information |
Beast2 | 2.7.6 | Linux | BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. | 3/27/2017 | 3/8/2024 | detailed information |
bed2diffs | 34ebbb6 | Linux | Computes the average genetic dissimilarity matrix from plink binary | 8/2/2024 | | 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 |
bettercallsal | 0.7.0 | Linux | an automated workflow to assign Salmonella serotype based on NCBI Pathogen Detection Project for Salmonella. | 4/24/2024 | | 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 |
bicycle | 1.8.2 | Linux | bisulfite-based methylcytosine caller | 10/23/2023 | | detailed information |
BiG-SCAPE | 1.1.5 | Linux | Biosynthetic Gene Similarity Clustering and Prospecting Engine | 12/4/2023 | | detailed information |
bigQF | 1.3-1 | Linux | R package for large quadratic forms | 2/26/2018 | | detailed information |
bigtools | 0.4.2 | Linux | Tools for reading and writing bigwig and bigbed files. | 5/16/2024 | | 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 |
biobakery | v3.0.0a7 | Linux | Microbial community profiling | 12/14/2021 | | 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 | 2.1.16 | 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 | 6/7/2024 | detailed information |
BioPerl | 1.7.8 | Linux | PERL library for general bioinformatics. | 12/13/2011 | 10/30/2022 | 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 |
biscuit | 1.5.0 | Linux | BISulfite-seq CUI Toolkit | 9/9/2024 | | detailed information |
Bismark | 0.24.1 | Linux | A bisulfite read mapper and methylation caller | 11/20/2012 | 6/16/2023 | detailed information |
Blackbird | 2019-11-25 | Linux | SV detection with 10X reads | 8/23/2022 | | detailed information |
blasr | 20180816 | Linux | The PacBio long read aligner | 9/24/2014 | 8/16/2018 | detailed information |
BLAST | 2.16.0 | Linux | Sequence alignment. | 12/13/2011 | 9/20/2024 | detailed information |
BLAST_to_BED | 20200928 | Linux | Parses a BLAST XML file and creates a BED file | 9/28/2020 | | detailed information |
blast2go | DB: August.2022: Software: v1.5.1 | Linux | Gene Ontology annotation and function enrichment analysis. | 4/15/2013 | 5/19/2021 | detailed information |
BLAT | 34 | Linux | Sequence alignment. | 12/13/2011 | 5/1/2012 | detailed information |
BlobToolKit | 2.6.3 | Linux | Visualisation, quality control and taxonomic partitioning of genome datasets | 9/30/2021 | | 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 |
bonito | 0.6.1 | Linux | A PyTorch Basecaller for Oxford Nanopore Reads. | 9/22/2022 | | detailed information |
Boost | 1.83.0 | Linux | Boost provides free peer-reviewed portable C++ source libraries. | 12/17/2014 | 12/1/2023 | detailed information |
Bowtie | 1.1.2 | Linux | An ultrafast, memory-efficient short read aligner. | 12/13/2011 | 3/22/2016 | detailed information |
Bowtie2 | 2.5.1 | Linux | An ultrafast, memory-efficient short read aligner. | 5/1/2012 | 8/15/2023 | detailed information |
BPGA | 1.3 | Linux | Comprehensive pan genome analysis of microorganisms | 10/25/2017 | | detailed information |
Bracken | 2.9 | Linux | A companion program to Kraken 1.0 or Kraken 2.0. | 2/12/2019 | 12/8/2023 | detailed information |
BRAKER | 3 | Linux | Uses genomic and RNA-Seq data to automatically generate full gene structure annotations in novel genome | 9/1/2019 | 10/17/2023 | detailed information |
BRAT-NextGen | 20150505 | Linux | NextGen software for Bayesian analysis of recombinations in whole-genome DNA sequence data, | 2/27/2019 | | detailed information |
BRBseqTools | 1.6 | Linux | A suite of tools for the pre-processing of BRB-seq data (bulk RNA-seq) | 7/5/2022 | | 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 |
BSBolt | 1.6.0 | Linux | A bisulfite sequencing analysis platform | 9/9/2024 | | detailed information |
bsmap | 2.74 | Linux | a short reads mapping program for bisulfite sequencing in DNA methylation study | 6/24/2023 | | detailed information |
BSseeker2 | 2.1.0 | Linux | Mapping the bisulfite-treated short reads | 1/23/2017 | | detailed information |
btyper3 | 3.4.0 | Linux | In silico taxonomic classification of Bacillus cereus group isolates using assembled genomes | 7/11/2024 | | detailed information |
BUSCO | 5.5.0 | Linux | Assessing genome assembly and annotation completeness. | 1/22/2016 | 8/31/2023 | detailed information |
BUSCO Phylogenomics | 2023-12-17 | Linux | Construct species phylogenies using BUSCO proteins | 12/17/2023 | | 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-mem2 | 2.2.1 | Linux | Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. | 9/26/2022 | | detailed information |
bwa-meth | v0.2.0 | Linux | aligners for BS-Seq | 1/17/2018 | | detailed information |
bwtool | 1.0 | Linux | A command-line utility for bigWig files | 1/26/2022 | | detailed information |
cactus | 2.6 | Linux | Cactus is a reference-free whole-genome multiple alignment program | 10/9/2018 | 7/24/2023 | detailed information |
CAFE | 4.2.1 | Linux | Analysis of gene Family Evolution | 12/3/2019 | | detailed information |
CAFE5 | 1.1 | Linux | Analysis of gene Family Evolution | 9/3/2024 | | detailed information |
caffe | 1.0 | Linux | A deep learning framework made with expression, speed, and modularity in mind | 11/28/2022 | | detailed information |
cagee | 1.1 | Linux | Computational Analysis of Gene Expression Evolution | 11/21/2022 | 4/3/2023 | detailed information |
canu | 2.2 | Linux | assemble pacbio or nanopore reads | 2/11/2016 | 11/17/2022 | detailed information |
Canvas | 1.40.0 | Linux | Canvas Copy Number Variant Caller | 1/24/2024 | | detailed information |
CAP3 | 12/21/07 | Linux | A DNA Sequence Assembly Program | 4/4/2014 | | detailed information |
caper | 1.5.1 | Linux | Cromwell Assisted Pipeline ExecutoR | 5/4/2021 | | detailed information |
CarveMe | 1.5.2 | 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 | 8/4/2023 | detailed information |
catch | 1.4.0 | Linux | Compact Aggregation of Targets for Comprehensive Hybridization | 9/22/2021 | | 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 |
CCMetagen | 1.4 | Linux | CCMetagen processes sequence alignments produced with KMA. | 1/12/2022 | | 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 |
cdo | 2.4.2 | Linux | A collection of command line Operators to manipulate and analyse Climate and NWP model Data. | 10/26/2023 | 6/23/2024 | 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 | 8.0.1 | Linux | A set of analysis pipelines that perform sample demultiplexing, barcode processing, and single cell 3’ gene counting. | 5/15/2017 | 7/5/2024 | detailed information |
cellranger-arc | 2.0.2 | 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 | 12/7/2023 | detailed information |
cellranger-atac | 2.1.9 | Linux | Set of analysis pipelines that process Chromium Single Cell ATAC data | 4/1/2019 | 10/2/2023 | 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 | 1.2.2 | Linux | CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes | 10/11/2016 | 2/18/2023 | detailed information |
CheckM2 | 1.0.1 | Linux | Rapid assessment of genome bin quality using machine learning. | 5/31/2023 | | detailed information |
chimera | 1.16 | Linux | Interactive visualization and analysis of molecular structures and related data. | 3/17/2019 | 2/6/2023 | detailed information |
ChimeraTE | 1.2 | Linux | T detect chimeric transcripts derived from genes and transposable elements (TEs). | 7/23/2024 | | detailed information |
chimerax | 1.7.1 | Linux | Molecular visualization program | 8/31/2023 | 4/29/2024 | detailed information |
chip-seq-pipeline | 2.1.6 | Linux | ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline | 6/2/2022 | | 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 | 0.69-9 | Linux | Circos is a software package for visualizing data and information. | 3/24/2015 | 11/6/2023 | 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 | 1.4.5 | Linux | Count antibody TAGS from a CITE-seq and/or cell hashing experiment. | 5/14/2020 | 9/18/2023 | detailed information |
ClermonTyping | 20220304 | Linux | Escherichia genus strain phylotyping | 3/4/2022 | | 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 | 1.18.0 | Linux | Optimised consensus clustering of one or more heterogeneous datasets. | 11/27/2019 | 6/22/2023 | 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 | 3.22.0-rc1 | Linux | CMake is an open-source, cross-platform family of tools designed to build, test and package software | 5/22/2017 | 10/20/2021 | detailed information |
CMSeq | 1.0.4 | Linux | CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus. | 8/23/2022 | | detailed information |
CNVnator | 0.4.1 | Linux | A tool for CNV discovery and genotyping from depth of read mapping | 6/23/2015 | 9/5/2023 | detailed information |
coinfinder | 1.2.0 | Linux | detects genes which associate and dissociate with other genes more often than expected by chance in pangenomes | 4/4/2023 | | detailed information |
colabfold | 1.5.5 | Linux | a variation of alphafold | 12/5/2022 | 3/24/2024 | detailed information |
CombFold | 20241209 | Linux | Predicts the structure of large protein complexes starting from the sequences of chains in the complex | 2/9/2024 | | detailed information |
Comparative-Annotation-Toolkit | 0.1-2 | Linux | Comparative-Annotation-Toolkit | 3/21/2024 | | 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 |
Cooler | 0.9.3 | Linux | Scalable quantitative maps. | 6/30/2021 | 5/8/2024 | 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 |
CoverM | v0.6.1 | Linux | DNA read coverage and relative abundance calculator focused on metagenomics applications. | 2/9/2022 | | detailed information |