Programs by Package

• ACeDB - Object-oriented biological database engine
• Babraham Bioinformatics -
• beagle - Phasing genotypes and imputing ungenotyped markers
• bioLegato - Programmable graphic user interface
• BIRCH - Biological Research Computing Hierarchy
• Castresana - Biodiversity and Evolution
• CCB - Johns Hopkins Center for Computational Biology
• cd-hit - cluster sequences and remove redundancy
• CLUSTAL - Multiple sequence alignment
• cutadapt - finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads
• Cytoscape - Cytoscape
• dapple - Image Analysis for DNA Microarrays
• Darling Lab - Computational Genomics
• DIALIGN - Multiple sequence alignment
• DTU_Health_Tech -
• Durand -
• EBI - Sequence chromatogram viewer
• EdwardsLab -
• EMBOSS - General sequence analysis
• FASTA - Pairwise and global similarity searches
• forester - Programs and API for phylogeny
• FSAP - Sequence analysis tools
• GDE - Genetic Data Environment
• genographer - Score markers from gel images
• GSC - UBC Michael Smith Genome Sciences Centre
• HTSLIB - Libraries for High Throughput Sequencing reads
• jellyfish - Fast, Parallel k-mer Counting for DNA
• LAST - Genome-Scale Sequence Comparison
• MAFFT - Multiple sequence alignment by fast Fourier Transformation
• MAGIC - MicroArray Genome Imaging & Clustering
• Mapmaker - Mapping with molecular and phenotypic markers
• MBCRR - Sequence analysis
• MCLAMP - Multiple alignment viewer
• Mesquite - A modular system for evolutionary analysis
• mourisl -
• MrBayes - Bayesian inference of phylogeny
• MWC - Oligonucleotide Molecular Weight Calculator
• NCBI - Database tools - Natl. Ctr. for Biotech. Information
• NCBI-edirect - Entrez Direct: E-utilities on the command line
• OSP - Oligonucleotide design
• pal2nal -
• PHYLIP - Package for Inferring Phylogenies
• PHYLO_WIN - Phylogenetic analysis
• pigz -
• pollux - DNA sequence read correction for all sequencing platforms
• PRIMER3 - Oligonucleotide design
• READSEQ - Sequence format translator
• Saint Petersberg Algorithmic Biology Lab -
• Salmon -
• SangerSeqTools - Package for visualizing sequence alignments
• SeqKit -
• SOAP -
• STEM - Short Time-series Expression Miner
• TIGR - J. Craig Venter Institute (TIGR)
• TIGR-TM4 - TIGR Microarray programs
• transrate - de-novo transcriptome assembly quality analysis
• Trimmomatic -
• Trinity - RNA-Seq De novo Assembly
• Ugene - Unipro Ugene - comprehensive bioinformatics package
• vanilla - phylogeny tools
• WebLogo - Create sequence logos
• weighbor - weighted neighbor-joining
• Wellcome_Trust_Sanger_Institute - Genomics Applications
• XLANDSCAPE - Find motifs in a group of sequences
• XYLEM - Create and manipulate database subsets
• Zmasek - Programs of Christian Zmasek