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

aaindexAmino acid indices and similarity matrices
abyssAssembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
amapProtein multiple-alignment-based sequence annealing
augustusEukaryotic gene predictor
bamtoolsA programmer's API and an end-user's toolkit for handling BAM files
bcftoolsUtilities for variant calling and manipulating VCF and BCF files
bedtoolsTools for manipulation and analysis of BED, GFF/GTF, VCF, SAM/BAM file formats
bfastBlat-like Fast Accurate Search Tool
biogrepMultithreaded tool for matching large sets of patterns against biosequence DBs
bioperlPerl tools for bioinformatics - Core modules
bioperl-dbPerl tools for bioinformatics - Perl API that accesses the BioSQL schema
bioperl-networkPerl tools for bioinformatics - Analysis of protein-protein interaction networks
bioperl-runPerl wrapper modules for key bioinformatics applications
biopythonPython modules for computational molecular biology
biosqlA generic bioinformatics relational database model
blatThe BLAST-Like Alignment Tool, a fast genomic sequence aligner
bowtiePopular short read aligner for Next-generation sequencing data
bwaBurrows-Wheeler Alignment Tool, a fast short genomic sequence aligner
cd-hitClustering Database at High Identity with Tolerance
clustal-omegaScalable multiple alignment of protein sequences
clustalwGeneral purpose multiple alignment program for DNA and proteins
clustalw-mpiAn MPI implemention of the ClustalW general purpose multiple alignment algorithm
clustalxGraphical interface for the ClustalW multiple alignment program
cutgCodon usage tables calculated from GenBank
dialign2Multiple sequence alignment
dialign-txGreedy and progressive approaches for segment-based multiple sequence alignment
elphEstimated Locations of Pattern Hits - Motif finder program
embassyA meta-package for installing all EMBASSY packages (EMBOSS add-ons)
embassy-cbstoolsEMBOSS integrated version of Applications from the CBS group
embassy-clustalomegaEMBOSS integrated version of Clustal Omega - Multiple Sequence Alignment
embassy-domainatrixEMBOSS integrated version of Protein domain analysis add-on package
embassy-domalignEMBOSS integrated version of Protein domain alignment add-on package
embassy-domsearchEMBOSS integrated version of Protein domain search add-on package
embassy-emnuEMBOSS integrated version of Simple menu of EMBOSS applications
embassy-esim4EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA
embassy-hmmerEMBOSS integrated version of HMMER wrapper - sequence analysis with profile HMMs
embassy-iprscanEMBOSS integrated version of InterProScan motif detection add-on package
embassy-mseEMBOSS integrated version of MSE - Multiple Sequence Screen Editor
embassy-phylipnewEMBOSS integrated version of The Phylogeny Inference Package
embassy-signatureEMBOSS integrated version of Protein signature add-on package
embassy-structureEMBOSS integrated version of Protein structure add-on package
embassy-topoEMBOSS integrated version of Transmembrane protein display
embassy-viennaEMBOSS integrated version of Vienna RNA package - RNA folding
embossThe European Molecular Biology Open Software Suite - A sequence analysis package
eugeneProkaryotic and Eukaryotic gene predictor
exonerateGeneric tool for pairwise sequence comparison
fastaFASTA is a DNA and Protein sequence alignment software package
fasttreeFast inference of approximately-maximum-likelihood phylogenetic trees
fastx_toolkitTools for Short Read FASTA/FASTQ file processing
finchtvGraphical viewer for chromatogram files
foldingathomeFolding@Home is a distributed computing project for protein folding
glimmerAn HMM-based microbial gene finding system from TIGR
glimmerhmmA eukaryotic gene finding system from TIGR
gmapA Genomic Mapping and Alignment Program for mRNA and EST Sequences
hmmerSequence analysis using profile hidden Markov models
iederaSubset seed design tool for DNA sequence alignment
infernalInference of RNA alignments
iqpnniImportant Quartet Puzzling and NNI Operation
kalignGlobal and progressive multiple sequence alignment
kallistoNear-optimal RNA-Seq quantification
laganThe LAGAN suite of tools for whole-genome multiple alignment of genomic DNA
libgtextutilsGordon Text utils Library
mafftMultiple sequence alignments using a variety of algorithms
maqMapping and Assembly with Qualities, mapping NGS reads to reference genomes
maqviewGUI for sci-biology/maq, a short read mapping assembler
mclA Markov Cluster Algorithm implementation
mosaikA reference-guided aligner for next-generation sequencing technologies
mothurA suite of algorithms for ecological bioinformatics
mrbayesBayesian Inference of Phylogeny
mummerA rapid whole genome aligner
muscleMultiple sequence comparison by log-expectation
newick-utilsTools for processing phylogenetic trees
palsPairwise Aligner for Long Sequences
pamlPhylogenetic Analysis by Maximum Likelihood
phylipThe PHYLogeny Inference Package
phymlEstimation of large phylogenies by maximum likelihood
pilerAnalysis of repetitive DNA found in genome sequences
pilercrAnalysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)
plinkWhole genome association analysis toolset
poaFast multiple sequence alignments using partial-order graphs
prankProbabilistic Alignment Kit
primer3Primer Design for PCR reactions
printsA protein motif fingerprint database
probconsProbabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
prodigalProkaryotic Dynamic Programming Genefinding Algorithm
profphdSecondary structure and solvent accessibility predictor
prositeA protein families and domains database
pysamPython interface for the SAM/BAM sequence alignment and mapping format
qrnaPrototype ncRNA genefinder
raxmlSequential, Parallel & Distributed Inference of Large Phylogenetic Trees
rebaseA restriction enzyme database
reconAutomated de novo identification of repeat families from genomic sequences
rnaviewGenerates 2D displays of RNA/DNA secondary structures with tertiary interactions
samtoolsUtilities for analysing and manipulating the SAM/BAM alignment formats
seaviewA graphical multiple sequence alignment editor
seqanC++ Sequence Analysis Library
sibsim4A rewrite and improvement upon sim4, a DNA-mRNA aligner
sim4A program to align cDNA and genomic DNA
STARSTAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays
strideProtein secondary structure assignment from atomic coordinates
t-coffeeA multiple sequence alignment package
tree-puzzleMaximum likelihood analysis for nucleotide, amino acid, and two-state data
treeviewxA phylogenetic tree viewer
trfTandem Repeats Finder
trnascan-setRNA detection in large-scale genome sequences
uchimeFast, accurate chimera detection
ucsc-genome-browserThe UCSC genome browser suite, also known as Jim Kent's library and GoldenPath
unafoldUnified Nucleic Acid Folding and hybridization package for local blast db maintainance
vcftoolsTools for working with VCF (Variant Call Format) files
velvetA sequence assembler for very short reads
wiseIntelligent algorithms for DNA searches
yassGenomic similarity search with multiple transition constrained spaced seeds


Packages: 113

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