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