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biology

Jul 20, 2023

  • Abyss - Assembly By Short Sequences parallel, paired-end sequence assembler
  • Ad2vcf - Add allelic depth info from a SAM stream to a VCF file
  • Artemis - DNA sequence viewer and annotation tool
  • Atac-seq - Metaport for ATAC-Seq analysis
  • Augustus - Genome annotation tool
  • Avida - Auto-adaptive genetic system designed for ALife research
  • Babel - Converts among various molecular file formats
  • Bamtools - API and toolkit for handling BAM files
  • Bamutil - Utilities for working with SAM/BAM files
  • Barrnap - BAsic Rapid Ribosomal RNA Predictor
  • Bbmap - BBMap short read aligner, and other bioinformatic tools
  • Bcf-score - Bcftools plugins for GWAS-VCF summary statistics files
  • Bcftools - Tools for manipulating next-generation sequencing data
  • Bedtools - Toolset for genome set arithmetic such as intersect, union
  • Bfc - Correct sequencing errors from Illumina sequencing data
  • Bifrost - Parallel construction, indexing and querying of de Bruijn graphs
  • Bio-mocha - Bcftools plugin for mosaic chromosomal alteration analysis
  • Bioawk - BWK awk modified for biological data
  • Biococoa - Bioinformatics framework
  • Biolibc-tools - High-performance bioinformatics tools based on biolibc
  • Biolibc - Low-level high-performance bioinformatics library
  • Bioparser - C++ header-only parsing library for several formats in bioinformatics
  • Biosig - Library for reading and writing different biosignal data format
  • Biosoup - Collection of C++ header-only data structures for bioinformatics
  • Biostar-tools - Meta-port for Biostar Handbook tools
  • Bolt-lmm - Mixed model association testing and variance component analysis
  • Bowtie - Ultrafast, memory-efficient short read aligner
  • Bowtie2 - Ultrafast, memory-efficient short read aligner
  • Bwa - Burrows-Wheeler sequence aligner
  • Canu - Single molecule sequence assembler
  • Cd-hit - Clustering and comparing protein or nucleotide sequences
  • Cdbfasta - Fast indexing and retrieval of FASTA records from flat file databases
  • Checkm - Quality assessment tool for the microbial genomes
  • Chip-seq - Metaport for ChIP-Seq analysis
  • Clustal-omega - Multiple alignment of nucleic acid and protein, replaces clustalw
  • Clustalw - Multiple alignment program for DNA or proteins
  • Consed - Graphical tool for editing Phrap assemblies
  • Cufflinks - Cufflinks assembles transcripts, estimates their abundance, etc
  • Cytoscape - Software to visualize molecular interaction networks, gene expression
  • Ddocent - Bash pipeline for RAD sequencing
  • Diamond - BLAST-compatible local sequence aligner
  • Dsr-pdb - Simple C++ PDB reader (reads the protein description format)
  • Edlib - Fast C++ library for sequence alignment using edit distance
  • Emboss - Collection of open source tools for genetic sequence analysis
  • Erminej - Analyses of gene sets such as gene expression profiling studies
  • Exonerate - Generic tool for sequence alignment
  • Fasda - Fast and simple differential analysis
  • Fasta - Collection of programs for searching DNA and protein databases
  • Fasta3 - Collection of programs for searching DNA and protein databases
  • Fastahack - Utility for indexing and sequence extraction from FASTA files
  • Fastdnaml - Faster DNAML, makes phylogenetic trees using maximum likelihood
  • Fastool - Simple and quick FastQ and FastA tool for file reading and conversion
  • Fastp - Ultra-fast all-in-one FASTQ preprocessor
  • Fastq-trim - Lightening fast sequence read trimmer
  • Fastqc - Quality control tool for high throughput sequence data
  • Fasttree - Approximately-maximum-likelihood phylogenetic trees from alignments
  • Fastx-toolkit - CLI tools for Short-Reads FASTA/FASTQ files preprocessing
  • Figtree - Graphical viewer of phylogenetic trees
  • Flash - Fast Length Adjustment of SHort reads
  • Fluctuate - Program to fit population models
  • Freebayes - Bayesian haplotype-based polymorphism discovery and genotyping
  • Garlic - Molecular viewer, editor, and visualization program
  • Gatk - Variant discovery in high-throughput sequencing data
  • Gcta - Genome-wide Complex Trait Analysis
  • Gemma - Genome-wide Efficient Mixed Model Association
  • Generand - Generate random genomic data in FASTA/FASTQ, SAM, or VCF format
  • Gff2ps - Convert gff-formatted genomic data sets to PostScript
  • Gffread - GFF/GTF format conversions, filtering, FASTA extraction, etc
  • Gmap - Genomic Mapping and Alignment Program for mRNA and EST Sequences
  • Gperiodic - Displays a periodic table of the elements
  • Graphlan - High-quality circular representations of taxonomic, phylogenetic trees
  • Groopm - Metagenomic binning suite
  • Haplohseq - Identify regions of allelic imbalance
  • Hhsuite - Remote protein homology detection suite
  • Hisat2 - Alignment program for mapping next-generation sequencing reads
  • Hmmer - Profile hidden Markov models for biological sequence analysis
  • Htslib - C library for high-throughput sequencing data formats
  • Hyphy - Hypothesis testing using Phylogenies
  • Igv - Visualization tool for genomic datasets
  • Infernal - Search sequence databases for structural RNA homologs
  • Iolib - General purpose trace file (and Experiment File) reading interface
  • Iqtree - Efficient phylogenomic software by maximum likelihood
  • Jalview - Viewer and editor for multiple sequence alignments
  • Jellyfish - Fast, memory-efficient counting of k-mers in DNA
  • Kallisto - Quantify abundances of transcripts from RNA-Seq data
  • Kmcp - Accurate metagenomic profiling & fast large-scale genome searching
  • Lamarc - Package of programs for computing population parameters
  • Libbigwig - C library for handling bigWig files (containing genomic data)
  • Libcombine - C++ library for working with the COMBINE archive format
  • Libgff - GFF/GTF parsing library based on GCLib
  • Libgtextutils - Gordon's text utilities
  • Libneurosim - Common interfaces for neuronal simulators
  • Libnuml - C++ library for Numerical Markup Language
  • Libsbml - API Library for Working with SBML File
  • Libsedml - C++ SED-ML library
  • Linux-foldingathome - Folding@home Client
  • Locarna - LocARNA provides several tools for the structural analysis of RNA
  • Mafft - Multiple alignment program for amino acid or nucleotide sequences
  • Mapm3 - Constructs linkage maps of markers segregating in experimental crosses
  • Mashmap - Fast approximate aligner for long DNA sequences
  • Megahit - Ultra-fast single-node large and complex metagenomics assembly
  • Metaeuk - Gene discovery and annotation for large-scale eukaryotic metagenomics
  • Migrate - Program to estimate population sizes and migration rates
  • Minimap2 - Pairwise aligner for genomic and spliced nucleotide sequences
  • Mmseqs2 - Ultra fast and sensitive sequence search and clustering suite
  • Molden - Display molecular orbitals and electron densities in 2D and 3D
  • Mothur - Software for bioinformatics of the microbial ecology community
  • Mrbayes - Bayesian inference of phylogeny
  • Mummer - Modular system for rapid whole genome alignment
  • Muscle - MUltiple Sequence Comparison by Log-Expectation
  • Ncbi-blast+ - NCBI implementation of Basic Local Alignment Search Tool
  • Ncbi-cxx-toolkit - NCBI C++ Toolkit
  • Ncbi-entrez-direct - Access to the NCBI's suite of interconnected databases
  • Ncbi-toolkit - NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
  • Ncbi-vdb - NCBI's virtualized back-end for accessing Sequence Read Archive
  • Ngs-sdk - Tools and libraries for using data in the INSDC Sequence Read Archives
  • P5-aceperl - Perl5 interface to the ACEDB genome database system
  • P5-bio-asn1-entrezgene - Regular expression-based Perl Parser for NCBI Entrez Gene
  • P5-bio-cluster - BioPerl cluster modules
  • P5-bio-coordinate - Modules for working with biological coordinates
  • P5-bio-db-embl - Database object interface for EMBL entry retrieval
  • P5-bio-db-ncbihelper - Collection of routines useful for queries to NCBI databases
  • P5-bio-das-lite - Perl extension for the DAS (HTTP+XML) Protocol
  • P5-bio-das - Client-side library for Distributed Genome Annotation System
  • P5-bio-featureio - Handler for FeatureIO
  • P5-bio-gff3 - Fast low-level functions for parsing and formatting GFF3
  • P5-bio-glite - Perl Interface to G-language
  • P5-bio-graphics - Generate GD Images of BioSeq Objects
  • P5-bio-magetab - Data model and utility API for the MAGE-TAB format
  • P5-bio-nexus - Object-oriented Perl API for the NEXUS file format
  • P5-bio-phylo - Phylogenetic analysis using Perl
  • P5-bio-scf - Read and Update SCF Chromatographic Sequence Files
  • P5-bio-variation - BioPerl variation-related functionality
  • P5-bioperl-run - Wrapper modules for common bioinformatics tools
  • P5-bioperl - Collection of Perl modules for bioinformatics
  • P5-trimgalore - Wrapper around Cutadapt and FastQC for adapter and quality trimming
  • P5-transdecoder - Identify candidate coding regions within transcript sequences
  • Paml - Phylogenetic Analysis by Maximum Likelihood (PAML)
  • Pbbam - PacBio BAM C++ library, with SWIG bindings
  • Pbcopper - Core C++ library for Pacific Biosciences tools
  • Pbseqan - Pacific Biosciences patched and stripped down SeqAn
  • Peak-classifier - Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
  • Pear-merger - Memory-efficient and highly accurate paired-end read merger
  • Phrap - Program for assembling shotgun DNA sequence data
  • Phred - Base calling and quality value assignment on DNA sequencing
  • Phyml - Simple, fast, and accurate algorithm to estimate large phylogenies
  • Picard-tools - CLI tools for manipulating high-throughput sequencing (HTS) data
  • Plink - Whole genome association analysis toolset
  • Plinkseq - Toolset for working with human genetic variation data
  • Pooler - Optimise DNA sequencing primer-set combinations
  • Primer3 - Primer3 helps to choose primers for PCR reactions
  • Prodigal - Protein-coding gene prediction for prokaryotic genomes
  • Prodigy-lig - Prediction of protein-small molecule binding affinities
  • Protomol - OO, component based, framework for molecular dynamics (MD) simulations
  • Psi88 - Plotting wavefunctions (molecular orbitals) in 3D
  • Py-genesis-pyapi - API for the Genesis platform for genetics information processing
  • Py-pysces - Python Simulator for Cellular Systems
  • Py-bcbio-gff - Read and write Generic Feature Format (GFF) with Biopython integration
  • Py-biom-format - Biological Observation Matrix (BIOM) Format Project
  • Py-biopython - Collection of Python modules for bioinformatics
  • Py-biosig - Library for reading and writing different biosignal data format
  • Py-bx-python - Python module for reading, manipulating and writing genomic data sets
  • Py-crossmap - Lift over genomics coordinates between assemblies
  • Py-cutadapt - Trim adapters from high-throughput sequencing reads
  • Py-deeptools - User-friendly tools for exploring deep-sequencing data
  • Py-deeptoolsintervals - Python interface for deepTools interval trees
  • Py-dna-features-viewer - Python library to visualize DNA features, e.g. GenBank or Gff files
  • Py-dnaio - Read and write FASTQ and FASTA
  • Py-ete3 - Framework for the analysis and visualization of trees
  • Py-gffutils - Work with GFF and GTF files in a flexible database framework
  • Py-goatools - Tools for processing and visualizing Gene Ontology terms
  • Py-gtfparse - Parsing tools for GTF (gene transfer format) files
  • Py-hits - Utilities for processing high-throughput sequencing experiments
  • Py-libnuml - Numerical Markup Language for Python
  • Py-libsedml - SED-ML library for Python
  • Py-loompy - Work with .loom files for single-cell RNA-seq data
  • Py-macs2 - Identify transcription factor binding sites
  • Py-mrcfile - MRC file I/O library which is used in structural biology
  • Py-multiqc - Aggregate bioinformatics analysis reports across samples and tools
  • Py-ont-fast5-api - Interface to HDF5 files in Oxford Nanopore .fast5 format
  • Py-orange3-bioinformatics - Orange add-on providing common functionality for bioinformatics
  • Py-orange3-single-cell - Orange add-on for gene expression of single cell data
  • Py-pandas-charm - Library for getting character matrices into and out of pandas
  • Py-py2bit - Python interface for 2bit packed nucleotide files
  • Py-pybigwig - Python access to bigWig files using libBigWig
  • Py-pyfaidx - Efficient pythonic random access to fasta subsequences
  • Py-pyrodigal - Python binding for Prodigal, an ORF finder for genomes and metagenomes
  • Py-pysam - Python module for reading, manipulating and writing genomic data sets
  • Py-python-libsbml - LibSBML Python API
  • Py-pywgsim - Modified wgsim genomic data simulator
  • Py-resdk - Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics
  • Py-scikit-bio - Data structures, algorithms, educational resources for bioinformatics
  • Py-valerius - Python bioinformatics tools
  • Py-xenapython - API for Xena Hub to access genetic information shared through the hub
  • Pycogent - Toolkit for statistical analysis of biological sequences
  • Pyfasta - Fast, memory-efficient, pythonic access to fasta sequence files
  • Python-nexus - Generic nexus file format reader for python
  • Rainbow - Efficient clustering and assembling of short reads, especially for RAD
  • Rampler - Standalone module for sampling genomic sequences
  • Readseq - Read and reformat biosequences, Java command-line version
  • Recombine - Program to fit population models across sites
  • Rna-seq - Metaport for RNA-Seq analysis
  • Ruby-bio - Integrated environment for Bioinformatics written in Ruby
  • Rubygem-bio-executables - Collection of miscellaneous utilities for bioinformatics
  • Rubygem-bio-old-biofetch-emulator - Emulate BioFetch object
  • Rubygem-bio-shell - Command-line interface on BioRuby
  • Rubygem-bio - Integrated environment for Bioinformatics written in Ruby
  • Sam2pairwise - Show pairwise alignment for each read in a SAM file
  • Samtools - Tools for manipulating next-generation sequencing data
  • Scrm - Coalescent simulator for biological sequences
  • Seaview - Multiple DNA/protein sequence alignment editor
  • Seqan-apps - Official bioinformatic applications based on the SeqAn library
  • Seqan - C++ sequence analysis template library
  • Seqan1 - C++ Sequence Analysis Library
  • Seqan3 - C++ header-only library for biological sequence analysis
  • Seqio - Set of C functions which can read/write biological sequence files
  • Seqkit - Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  • Seqtk - Tool for processing sequences in FASTA/FASTQ format
  • Seqtools - Tools for visualising sequence alignments
  • Sigviewer - Viewing application for biosignals
  • Sim4 - Algorithm for aligning expressed DNA with genomic sequences
  • Slclust - Single-linkage clustering with Jaccard similarity
  • Smithwaterman - Smith-waterman-gotoh alignment algorithm
  • Snpeff - Genetic variant annotation and effect prediction toolbox
  • Spoa - C++ implementation of the partial order alignment (POA) algorithm
  • Sra-tools - NCBI's toolkit for handling data in INSDC Sequence Read Archives
  • Stacks - Software pipeline for building loci from short-read sequences
  • Star - Spliced Transcripts Alignment to a Reference
  • Stringtie - Transcript assembly and quantification for RNA-seq
  • Subread - High-performance read alignment, quantification and mutation discovery
  • Trnascan-se - Searching for tRNA genes in genomic sequence
  • T_coffee - Multiple DNA or protein sequence alignment package
  • Tabixpp - C++ wrapper to tabix indexer
  • Taxonkit - Practical and efficient NCBI taxonomy toolkit
  • Tophat - Fast splice junction mapper for RNA-Seq reads
  • Treekin - Efficient computation of RNA folding dynamics
  • Treepuzzle - Maximum likelihood phylogeny reconstruction using quartets
  • Trimadap - Trim adapter sequences from Illumina data using heuristic rules
  • Trimmomatic - Flexible read trimming tool for Illumina NGS data
  • Ucsc-userapps - Command line tools from the UCSC Genome Browser project
  • Ugene - Integrated bioinformatics toolkit
  • Unanimity - Pacific Biosciences consensus library and applications
  • Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
  • Vcf-split - Split a multi-sample VCF into single-sample VCFs
  • Vcf2hap - Generate .hap file from VCF for haplohseq
  • Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
  • Vcftools - Tools for working with VCF genomics files
  • Velvet - Sequence assembler for very short reads
  • Viennarna - Alignment tools for the structural analysis of RNA
  • Vsearch - Versatile open-source tool for metagenomics
  • Vt - Discovers short variants from Next Generation Sequencing data
  • Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
  • Wise - Intelligent algorithms for DNA searches
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