| aaindex | Amino acid indices and similarity matrices |
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| abyss | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
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| amap | Protein multiple-alignment-based sequence annealing |
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| augustus | Eukaryotic gene predictor |
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| bamtools | A programmer's API and an end-user's toolkit for handling BAM files |
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| bcftools | Utilities for variant calling and manipulating VCF and BCF files |
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| bedtools | Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats |
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| bfast | Blat-like Fast Accurate Search Tool |
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| biogrep | Multithreaded tool for matching large sets of patterns against biosequence DBs |
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| bioperl | Perl tools for bioinformatics - Core modules |
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| bioperl-db | Perl tools for bioinformatics - Perl API that accesses the BioSQL schema |
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| bioperl-network | Perl tools for bioinformatics - Analysis of protein-protein interaction networks |
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| bioperl-run | Perl wrapper modules for key bioinformatics applications |
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| biopython | Python modules for computational molecular biology |
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| biosql | A generic bioinformatics relational database model |
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| blat | The BLAST-Like Alignment Tool, a fast genomic sequence aligner |
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| bowtie | Popular short read aligner for Next-generation sequencing data |
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| bwa | Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner |
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| cd-hit | Clustering Database at High Identity with Tolerance |
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| clustal-omega | Scalable multiple alignment of protein sequences |
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| clustalw | General purpose multiple alignment program for DNA and proteins |
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| clustalw-mpi | An MPI implemention of the ClustalW general purpose multiple alignment algorithm |
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| cutg | Codon usage tables calculated from GenBank |
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| dialign2 | Multiple sequence alignment |
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| dialign-tx | Greedy and progressive approaches for segment-based multiple sequence alignment |
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| elph | Estimated Locations of Pattern Hits - Motif finder program |
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| embassy | A meta-package for installing all EMBASSY packages (EMBOSS add-ons) |
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| embassy-cbstools | EMBOSS integrated version of Applications from the CBS group |
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| embassy-clustalomega | EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment |
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| embassy-domainatrix | EMBOSS integrated version of Protein domain analysis add-on package |
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| embassy-domalign | EMBOSS integrated version of Protein domain alignment add-on package |
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| embassy-domsearch | EMBOSS integrated version of Protein domain search add-on package |
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| embassy-emnu | EMBOSS integrated version of Simple menu of EMBOSS applications |
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| embassy-esim4 | EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA |
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| embassy-hmmer | EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs |
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| embassy-iprscan | EMBOSS integrated version of InterProScan motif detection add-on package |
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| embassy-mse | EMBOSS integrated version of MSE - Multiple Sequence Screen Editor |
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| embassy-phylipnew | EMBOSS integrated version of The Phylogeny Inference Package |
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| embassy-signature | EMBOSS integrated version of Protein signature add-on package |
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| embassy-structure | EMBOSS integrated version of Protein structure add-on package |
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| embassy-topo | EMBOSS integrated version of Transmembrane protein display |
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| embassy-vienna | EMBOSS integrated version of Vienna RNA package - RNA folding |
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| emboss | The European Molecular Biology Open Software Suite - A sequence analysis package |
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| eugene | Prokaryotic and Eukaryotic gene predictor |
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| exonerate | Generic tool for pairwise sequence comparison |
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| fasta | FASTA is a DNA and Protein sequence alignment software package |
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| fasttree | Fast inference of approximately-maximum-likelihood phylogenetic trees |
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| fastx_toolkit | Tools for Short Read FASTA/FASTQ file processing |
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| finchtv | Graphical viewer for chromatogram files |
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| foldingathome | Folding@Home is a distributed computing project for protein folding |
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| glimmer | An HMM-based microbial gene finding system from TIGR |
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| glimmerhmm | A eukaryotic gene finding system from TIGR |
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| gmap | A Genomic Mapping and Alignment Program for mRNA and EST Sequences |
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| hmmer | Sequence analysis using profile hidden Markov models |
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| iedera | Subset seed design tool for DNA sequence alignment |
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| infernal | Inference of RNA alignments |
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| iqpnni | Important Quartet Puzzling and NNI Operation |
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| kalign | Global and progressive multiple sequence alignment |
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| kallisto | Near-optimal RNA-Seq quantification |
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| lagan | The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA |
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| libgtextutils | Gordon Text utils Library |
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| mafft | Multiple sequence alignments using a variety of algorithms |
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| maq | Mapping and Assembly with Qualities, mapping NGS reads to reference genomes |
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| maqview | GUI for sci-biology/maq, a short read mapping assembler |
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| mcl | A Markov Cluster Algorithm implementation |
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| mosaik | A reference-guided aligner for next-generation sequencing technologies |
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| mothur | A suite of algorithms for ecological bioinformatics |
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| mrbayes | Bayesian Inference of Phylogeny |
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| mummer | A rapid whole genome aligner |
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| muscle | Multiple sequence comparison by log-expectation |
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| newick-utils | Tools for processing phylogenetic trees |
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| pals | Pairwise Aligner for Long Sequences |
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| paml | Phylogenetic Analysis by Maximum Likelihood |
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| phylip | The PHYLogeny Inference Package |
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| phyml | Estimation of large phylogenies by maximum likelihood |
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| piler | Analysis of repetitive DNA found in genome sequences |
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| pilercr | Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) |
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| plink | Whole genome association analysis toolset |
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| poa | Fast multiple sequence alignments using partial-order graphs |
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| prank | Probabilistic Alignment Kit |
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| primer3 | Primer Design for PCR reactions |
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| prints | A protein motif fingerprint database |
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| probcons | Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences |
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| prodigal | Prokaryotic Dynamic Programming Genefinding Algorithm |
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| profphd | Secondary structure and solvent accessibility predictor |
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| prosite | A protein families and domains database |
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| pysam | Python interface for the SAM/BAM sequence alignment and mapping format |
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| qrna | Prototype ncRNA genefinder |
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| raxml | Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees |
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| rebase | A restriction enzyme database |
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| recon | Automated de novo identification of repeat families from genomic sequences |
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| rnaview | Generates 2D displays of RNA/DNA secondary structures with tertiary interactions |
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| samtools | Utilities for analysing and manipulating the SAM/BAM alignment formats |
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| seaview | A graphical multiple sequence alignment editor |
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| seqan | C++ Sequence Analysis Library |
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| sibsim4 | A rewrite and improvement upon sim4, a DNA-mRNA aligner |
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| sim4 | A program to align cDNA and genomic DNA |
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| STAR | STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays |
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| stride | Protein secondary structure assignment from atomic coordinates |
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| t-coffee | A multiple sequence alignment package |
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| tree-puzzle | Maximum likelihood analysis for nucleotide, amino acid, and two-state data |
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| treeviewx | A phylogenetic tree viewer |
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| trf | Tandem Repeats Finder |
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| trnascan-se | tRNA detection in large-scale genome sequences |
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| uchime | Fast, accurate chimera detection |
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| ucsc-genome-browser | The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath |
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| unafold | Unified Nucleic Acid Folding and hybridization package |
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| update-blastdb | update_blastdb.pl for local blast db maintainance |
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| vcftools | Tools for working with VCF (Variant Call Format) files |
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| velvet | A sequence assembler for very short reads |
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| wise | Intelligent algorithms for DNA searches |
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| yass | Genomic similarity search with multiple transition constrained spaced seeds |
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Packages