Packages tagged bioinformatics

96 packages have this tag.

[Merge tag] (trustees only)

Related tags: library (78), gpl (64), program (51), bsd3 (16), mit (9), data-structures (6), formal-languages (6), lgpl (6), algorithms (5), benchmark (3), bindings (1), ffi (1), ...

Name
DLs
Rating
Description
Tags
Maintainer
ADPfusion1600.0Efficient, high-level dynamic programming. (algorithms, bioinformatics, bsd3, data-structures, formal-languages, library)ChristianHoener
ADPfusionSet100.0Dynamic programming for Set data structures. (algorithms, bioinformatics, bsd3, data-structures, formal-languages, library)ChristianHoener
AlignmentAlgorithms330.0Collection of alignment algorithms (algorithms, bioinformatics, data-structures, gpl, library, linguistics)ChristianHoener
BCMtools140.0Big Contact Map Tools (bioinformatics, library, mit, program)kaizhang
BioHMM1440.0Libary for Hidden Markov Models in HMMER3 format. (bioinformatics, gpl, library)FlorianEggenhofer
Biobase450.0Base library for bioinformatics (bioinformatics, gpl, library)ChristianHoener
BiobaseBlast170.0BLAST-related tools (bioinformatics, gpl, library)ChristianHoener
BiobaseDotP80.0Vienna / DotBracket / ExtSS parsers (bioinformatics, gpl, library)ChristianHoener
BiobaseFR3D320.0Importer for FR3D resources (bioinformatics, gpl, library)ChristianHoener
BiobaseFasta320.0conduit-based FASTA parser (bioinformatics, gpl, library, program)ChristianHoener
BiobaseInfernal1140.0Infernal data structures and tools (benchmark, bioinformatics, gpl, library, program)ChristianHoener
BiobaseMAF100.0Multiple Alignment Format (bioinformatics, gpl, library)ChristianHoener
BiobaseNewick150.0Newick file format parser. (bioinformatics, bsd3, library, program)ChristianHoener
BiobaseTrainingData350.0RNA folding training data (bioinformatics, gpl, library, program)ChristianHoener
BiobaseTurner870.0Import Turner RNA parameters (bioinformatics, gpl, library)ChristianHoener
BiobaseTypes460.0Collection of types for bioinformatics (bioinformatics, bsd3, data-structures, library)ChristianHoener
BiobaseVienna720.0Import Vienna energy parameters (bioinformatics, gpl, library)ChristianHoener
BiobaseXNA1960.0Efficient RNA/DNA representations (bioinformatics, gpl, library, program)ChristianHoener
BlastHTTP350.0Libary to interface with the NCBI blast REST interface (bioinformatics, gpl, library)FlorianEggenhofer
CMCompare290.0Infernal covariance model comparison (bioinformatics, gpl, library, program)ChristianHoener
ClustalParser630.0Libary for parsing Clustal tools output (bioinformatics, gpl, library, program)FlorianEggenhofer
DnaProteinAlignment70.0Frameshift-aware alignment of protein sequences with DNA sequences (bioinformatics, gpl, library, program)ChristianHoener
EntrezHTTP340.0Libary to interface with the NCBI Entrez REST service. (bioinformatics, gpl, library)FlorianEggenhofer
ForestStructures120.0Tree- and forest structures (benchmark, bioinformatics, bsd3, formal-languages, library)ChristianHoener
FormalGrammars550.0(Context-free) grammars in formal language theory (bioinformatics, formal-languages, gpl, library, program)ChristianHoener
Genbank260.0Libary for processing the NCBI genbank format (bioinformatics, gpl, library, program)FlorianEggenhofer
Gene-CluEDO190.0Hox gene clustering (bioinformatics, gpl, library, program)ChristianHoener
GenussFold100.0MCFGs for Genus-1 RNA Pseudoknots (bioinformatics, formal-languages, gpl, library, program)ChristianHoener
GrammarProducts350.0Grammar products and higher-dimensional grammars (bioinformatics, formal-languages, gpl, library)ChristianHoener
MC-Fold-DP180.0Folding algorithm based on nucleotide cyclic motifs. (bioinformatics, gpl, library, program)ChristianHoener
MutationOrder100.0Most likely order of mutation events in RNA (bioinformatics, gpl, library, program)ChristianHoener
Nussinov78200.0Nussinov78 using the ADPfusion library. (bioinformatics, gpl, library, program)ChristianHoener
PDBtools150.0A library for analysis of 3-D protein coordinates (bioinformatics, gpl, library)GrantRotskoff
RNAFold330.0RNA secondary structure prediction (bioinformatics, gpl, library, program)ChristianHoener
RNAFoldProgs170.0RNA secondary structure folding (bioinformatics, gpl, program)ChristianHoener
RNAdesign220.0Multi-target RNA sequence design (bioinformatics, gpl, library, program)ChristianHoener
RNAdraw60.0Draw RNA secondary structures (bioinformatics, gpl, library, program)ChristianHoener
RNAlien602.0Unsupervized construction of RNA family models (bioinformatics, gpl, library, program)FlorianEggenhofer
RNAwolf310.0RNA folding with non-canonical basepairs and base-triplets. (bioinformatics, gpl, library, program)ChristianHoener
SelectSequencesFromMSA130.0SelectSequences is a tool for selection of a represenative subset of sequences from a multiple sequence alignment in clustal format. (bioinformatics, gpl, library, program)FlorianEggenhofer
StockholmAlignment380.0Libary for Stockholm aligmnent format (bioinformatics, gpl, library)FlorianEggenhofer
Taxonomy200.0Libary for parsing, processing and vizualization of taxonomy data (bioinformatics, gpl, library)FlorianEggenhofer
TaxonomyTools120.0Tool for parsing, processing, comparing and visualizing taxonomy data (bioinformatics, gpl, program)FlorianEggenhofer
ViennaRNA-bindings450.0ViennaRNA v2 bindings (bindings, bioinformatics, ffi, library)ChristianHoener
ViennaRNAParser660.0Libary for parsing ViennaRNA package output (bioinformatics, gpl, library)FlorianEggenhofer
a50160.0Compare genome assemblies (bioinformatics, gpl, program)KetilMalde
adp-multi190.0ADP for multiple context-free languages (algorithms, bioinformatics, bsd3, data-structures, library)MaikRiechert
adp-multi-monadiccp110.0Subword construction in adp-multi using monadiccp (algorithms, bioinformatics, bsd3, data-structures, library)MaikRiechert
bamstats170.0A program to extract various information from BAM alignmnet files. (bioinformatics, gpl, library, program)KetilMalde
bio800.0A bioinformatics library (bioinformatics, lgpl, library)GwernBranwen, KetilMalde
bioace90.0Library for reading ace assembly files (bioinformatics, gpl, library)DanFornika
bioalign220.0Data structures and helper functions for calculating alignments (bioinformatics, gpl, library)DanFornika
biocore160.0A bioinformatics library (bioinformatics, lgpl, library)KetilMalde
biofasta130.0Library for reading fasta sequence files (bioinformatics, gpl, library)DanFornika
biofastq60.0A library for reading FASTQ files (bioinformatics, lgpl, library)KetilMalde
biohazard550.0bioinformatics support library (bioinformatics, bsd3, library)ustenzel
biophd320.0Library for reading phd sequence files (bioinformatics, gpl, library)DanFornika
biopsl190.0Library and executables for working with PSL files (bioinformatics, lgpl, library, program)KetilMalde
biosff310.0Library and executables for working with SFF files (bioinformatics, lgpl, library)KetilMalde
biostockholm340.0Parsing and rendering of Stockholm files (used by Pfam, Rfam and Infernal). (bioinformatics, bsd3, library)FelipeLessa
blastxml160.0Library for reading Blast XML output (bioinformatics, lgpl, library)KetilMalde
blosum150.0BLOSUM generator (bioinformatics, gpl, library, program)GregorySchwartz
clustertools160.0Tools for manipulating sequence clusters (bioinformatics, gpl, program)GwernBranwen, KetilMalde
cmv400.0Detailed visualization of CMs, HMMs and their comparisions (bioinformatics, gpl, library, program)FlorianEggenhofer
convert-annotation160.0Convert the annotation of a gene to another in a delimited file using a variety of different databases. (bioinformatics, gpl, library, program)GregorySchwartz
dephd280.0Analyze quality of nucleotide sequences. (bioinformatics, gpl, program)GwernBranwen, KetilMalde
diversity1020.0Quantify the diversity of a population (bioinformatics, gpl, library, program)GregorySchwartz
estreps140.0Repeats from ESTs (bioinformatics, gpl, program)GwernBranwen, KetilMalde
flower530.0Analyze 454 flowgrams (.SFF files) (bioinformatics, gpl, program)KetilMalde
flowsim260.0Simulate 454 pyrosequencing (bioinformatics, gpl, program)KetilMalde
gact70.0General Alignment Clustering Tool (bioinformatics, gpl, program)KetilMalde
hPDB570.0Protein Databank file format library (bioinformatics, bsd3, library)MichalGajda
hPDB-examples360.0Examples for hPDB library (bioinformatics, bsd3, program)MichalGajda
hTalos30.0Parser, print and manipulate structures in PDB file format. (bioinformatics, bsd3, library)MichalGajda
hemokit390.0Haskell port of the Emokit EEG project (benchmark, bioinformatics, library, mit, program)NiklasHambuechen, PatrickChilton
korfu70.0The Korfu ORF Utility (bioinformatics, gpl, program)KetilMalde
memexml60.0Library for reading Meme XML output (bioinformatics, bsd3, library)FlorianEggenhofer
mmtf60.0Macromolecular Transmission Format implementation (bioinformatics, bsd3, library)zmactep
modify-fasta180.0Modify fasta (and CLIP) files in several optional ways (bioinformatics, gpl, library, program)GregorySchwartz
phybin190.0Utility for clustering phylogenetic trees in Newick format based on Robinson-Foulds distance. (bioinformatics, bsd3, library, program)RyanNewton
rank-product180.0Find the rank product of a data set. (bioinformatics, gpl, library)GregorySchwartz
rbr60.0Mask nucleotide (EST) sequences in Fasta format (bioinformatics, gpl, program)GwernBranwen, KetilMalde
samtools280.0Binding to the C samtools library (bioinformatics, library, mit)NicholasIngolia
samtools-conduit70.0Conduit interface to SAM/BAM format files through samtools (bioinformatics, library, mit, program)NicholasIngolia
samtools-enumerator70.0Enumerator interface to SamTools library (bioinformatics, library, mit)NicholasIngolia
samtools-iteratee80.0Iteratee interface to SamTools library (bioinformatics, library, mit)NicholasIngolia
seqloc250.0Handle sequence locations for bioinformatics (bioinformatics, library, mit)NicholasIngolia
seqloc-datafiles120.0Read and write BED and GTF format genome annotations (bioinformatics, library, mit, program)NicholasIngolia
sgrep20.0Sgrep - grep Fasta files for sequences matching a regular expression (bioinformatics, gpl, program)KetilMalde
simseq40.0Simulate sequencing with different models for priming and errors (bioinformatics, gpl, program)GwernBranwen
smiles170.0 (bioinformatics, bsd3, library)fonturacetamum
trimpolya30.0Search for, annotate and trim poly-A tail (bioinformatics, gpl, program)KetilMalde
varan50.0Process mpileup output to identify significant differences (bioinformatics, gpl, program)KetilMalde
vcf62.0A package to parse VCF files inspired in similar python libraries (bioinformatics, library, mit)juanpaucar
xml2x150.0Convert BLAST output in XML format to CSV or HTML (bioinformatics, gpl, program)GwernBranwen, KetilMalde
xsact80.0Cluster EST sequences (bioinformatics, gpl, program)GwernBranwen, KetilMalde