The sci-biology category contains software that can be used in biological and related scientific environments.

All packages

aaindex Amino acid indices and similarity matrices
abyss Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpathslg De novo assembly of whole-genome shotgun microreads
amap Protein multiple-alignment-based sequence annealing
amos A Modular, Open-Source whole genome assembler
ApE A Plasmid Editor
arb Tools for DNA/RNA sequence database handling and phylogenetic analysis
ariadne Protein sequences and profiles comparison
augustus Eukaryotic gene predictor
bamtools A programmer's API and an end-user's toolkit for handling BAM files
beast-mcmc Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences
bedtools Tools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats
bfast Blat-like Fast Accurate Search Tool
biogrep Multithreaded tool for matching large sets of patterns against biosequence DBs
biopandas Molecular Structures in Pandas DataFrames
bioperl Perl tools for bioinformatics - Core modules
bioperl-db Perl tools for bioinformatics - Perl API that accesses the BioSQL schema
bioperl-network Perl tools for bioinformatics - Analysis of protein-protein interaction networks
bioperl-run Perl wrapper modules for key bioinformatics applications
biopython Python modules for computational molecular biology
bioruby An integrated environment for bioinformatics using the Ruby language
biosql A generic bioinformatics relational database model
blat The BLAST-Like Alignment Tool, a fast genomic sequence aligner
blossoc A linkage disequilibrium association mapping tool
bowtie Popular short read aligner for Next-generation sequencing data
bwa Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner
cd-hit Clustering Database at High Identity with Tolerance
clustal-omega Scalable multiple alignment of protein sequences
clustalw General purpose multiple alignment program for DNA and proteins
clustalw-mpi An MPI implemention of the ClustalW general purpose multiple alignment algorithm
clustalx Graphical interface for the ClustalW multiple alignment program
consed A genome sequence finishing program
cufflinks Transcript assembly and differential expression/regulation for RNA-Seq
cutg Codon usage tables calculated from GenBank
dialign-tx Greedy and progressive approaches for segment-based multiple sequence alignment
dialign2 Multiple sequence alignment
diya Do It Yourself Annotation, tools & libraries for sequence assembly & annotation
elph Estimated Locations of Pattern Hits - Motif finder program
embassy A meta-package for installing all EMBASSY packages (EMBOSS add-ons)
embassy-cbstools EMBOSS integrated version of Applications from the CBS group
embassy-clustalomega EMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment
embassy-domainatrix EMBOSS integrated version of Protein domain analysis add-on package
embassy-domalign EMBOSS integrated version of Protein domain alignment add-on package
embassy-domsearch EMBOSS integrated version of Protein domain search add-on package
embassy-emnu EMBOSS integrated version of Simple menu of EMBOSS applications
embassy-esim4 EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA
embassy-hmmer EMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs
embassy-iprscan EMBOSS integrated version of InterProScan motif detection add-on package
embassy-meme EMBOSS integrated version of MEME - Multiple Em for Motif Elicitation
embassy-mse EMBOSS integrated version of MSE - Multiple Sequence Screen Editor
embassy-phylipnew EMBOSS integrated version of The Phylogeny Inference Package
embassy-signature EMBOSS integrated version of Protein signature add-on package
embassy-structure EMBOSS integrated version of Protein structure add-on package
embassy-topo EMBOSS integrated version of Transmembrane protein display
embassy-vienna EMBOSS integrated version of Vienna RNA package - RNA folding
emboss The European Molecular Biology Open Software Suite - A sequence analysis package
eugene Prokaryotic and Eukaryotic gene predictor
exonerate Generic tool for pairwise sequence comparison
express Streaming RNA-Seq Analysis
fasta FASTA is a DNA and Protein sequence alignment software package
fasttree Fast inference of approximately-maximum-likelihood phylogenetic trees
finchtv Graphical viewer for chromatogram files
foldingathome Folding@Home is a distributed computing project for protein folding
gatk The Genome Analysis Toolkit
GBrowse Generic Model Organism Database Project - The Generic Genome Browser
gibbs Identify motifs, conserved regions, in DNA or protein sequences
glimmer An HMM-based microbial gene finding system from TIGR
glimmerhmm A eukaryotic gene finding system from TIGR
gmap A Genomic Mapping and Alignment Program for mRNA and EST Sequences
goby A DNA sequencing data management framework
goby-cpp A DNA sequencing data management framework - C/C++ API
hmmer Sequence analysis using profile hidden Markov models
iedera A subset seed design tool for DNA sequence alignment
infernal Inference of RNA alignments
iqpnni Important Quartet Puzzling and NNI Operation
kalign Global and progressive multiple sequence alignment
lagan The LAGAN suite of tools for whole-genome multiple alignment of genomic DNA
last Genome-scale comparison of biological sequences
mafft Multiple sequence alignments using a variety of algorithms
mammoth MAtching Molecular Models Obtained from THeory
maq Mapping and Assembly with Qualities, mapping NGS reads to reference genomes
maqview GUI for sci-biology/maq, a short read mapping assembler
mcl A Markov Cluster Algorithm implementation
meme The MEME/MAST system - Motif discovery and search
mira Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Illumina
mosaik A reference-guided aligner for next-generation sequencing technologies
mothur A suite of algorithms for ecological bioinformatics
mrbayes Bayesian Inference of Phylogeny
mummer A rapid whole genome aligner
muscle Multiple sequence comparison by log-expectation
ncbi-tools Development toolkit and applications for computational biology, including BLAST
newick-utils Tools for processing phylogenetic trees
njplot A phylogenetic tree drawing program which supports tree rooting
pals Pairwise Aligner for Long Sequences
paml Phylogenetic Analysis by Maximum Likelihood
phrap Shotgun assembly and alignment utilities
phred A base caller for Sanger DNA sequencing
phylip The PHYLogeny Inference Package
phyml Estimation of large phylogenies by maximum likelihood
picard Java-based command-line utilities that manipulate SAM files
piler Analysis of repetitive DNA found in genome sequences
pilercr Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)
plink Whole genome association analysis toolset
poa Fast multiple sequence alignments using partial-order graphs
prank Probabilistic Alignment Kit
primer3 Primer Design for PCR reactions
prints A protein motif fingerprint database
probcons Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
prodigal Prokaryotic Dynamic Programming Genefinding Algorithm
profphd Secondary structure and solvent accessibility predictor
prosite A protein families and domains database
psipred Protein Secondary Structure Prediction
pysam Python interface for the SAM/BAM sequence alignment and mapping format
qrna Prototype ncRNA genefinder
raxml Sequential, Parallel & Distributed Inference of Large Phylogenetic Trees
rebase A restriction enzyme database
recon Automated de novo identification of repeat families from genomic sequences
repeatmasker Screen DNA sequences for interspersed repeats and low complexity DNA
repeatmasker-libraries A special version of RepBase used by RepeatMasker
rmblast RepeatMasker compatible version of NCBI BLAST+
rnaview Generates 2D displays of RNA/DNA secondary structures with tertiary interactions
samtools Utilities for analysing and manipulating the SAM/BAM alignment formats
seaview A graphical multiple sequence alignment editor
seqan C++ Sequence Analysis Library
shrimp SHort Read Mapping Package
sibsim4 A rewrite and improvement upon sim4, a DNA-mRNA aligner
sim4 A program to align cDNA and genomic DNA
snpfile A library and API for manipulating large SNP datasets
stride Protein secondary structure assignment from atomic coordinates
t-coffee A multiple sequence alignment package
tophat Python-based splice junction mapper for RNA-Seq reads using bowtie2
transfac A database of eucaryotic transcription factors
tree-puzzle Maximum likelihood analysis for nucleotide, amino acid, and two-state data
treeviewx A phylogenetic tree viewer
trf Tandem Repeats Finder
trnascan-se tRNA detection in large-scale genome sequences
uchime Fast, accurate chimera detection
ucsc-genome-browser The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath
unafold Unified Nucleic Acid Folding and hybridization package
update-blastdb for local blast db maintainance
vaal Algorithm for detecting SNPs, indels, and other polymorphisms
vcftools Tools for working with VCF (Variant Call Format) files
velvet A sequence assembler for very short reads
vienna-rna RNA secondary structure prediction and comparison
wgs-assembler The Celera de novo whole-genome shotgun DNA sequence assembler, aka CABOG
wise Intelligent algorithms for DNA searches
yass Genomic similarity search with multiple transition constrained spaced seeds


147 Packages