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sci-biology/fastx_toolkit

Tools for Short Read FASTA/FASTQ file processing

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/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/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/mosaik

A reference-guided aligner for next-generation sequencing technologies

sci-biology/mothur

Suite of algorithms for ecological bioinformatics

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/probcons

Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

sci-biology/prodigal

Prokaryotic Dynamic Programming Genefinding Algorithm

sci-biology/raxml

Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees

sci-biology/recon

Automated de novo identification of repeat families from genomic sequences

sci-biology/samtools

Utilities for analysing and manipulating the SAM/BAM alignment formats

sci-biology/seaview

A graphical multiple sequence alignment editor

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/trnascan-se

tRNA detection in large-scale genome sequences

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/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

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/bioperl

Perl tools for bioinformatics - Core modules