Packages tagged bioinformatics

118 packages have this tag.

[Merge tag] (trustees only)

Related tags: library (98), program (64), gpl (59), bsd3 (22), mit (9), formal-languages (8), data-structures (6), algorithms (5), ab1 (1), abif (1), bindings (1), chromatogram (1), ...

Name
DLs
Rating
Description
Tags
Last U/L
Maintainer
ADPfusion4830.0Efficient, high-level dynamic programming. (algorithms, bioinformatics, bsd3, data-structures, formal-languages, library)2017-03-06ChristianHoener
ADPfusionForest290.0Dynamic programming on tree and forest structures (bioinformatics, bsd3, formal-languages, library)2017-11-23ChristianHoener
ADPfusionSet730.0Dynamic programming for Set data structures. (algorithms, bioinformatics, bsd3, data-structures, formal-languages, library)2017-10-19ChristianHoener
AlignmentAlgorithms1290.0Collection of alignment algorithms (algorithms, bioinformatics, data-structures, gpl, library, linguistics)2017-03-14ChristianHoener
BCMtools420.0Big Contact Map Tools (bioinformatics, library, mit, program)2015-05-05kaizhang
BioHMM4890.0Libary for Hidden Markov Models in HMMER3 format. (bioinformatics, gpl, library)2017-06-09FlorianEggenhofer
Biobase1000.0Base library for bioinformatics (bioinformatics, gpl, library)2011-04-08ChristianHoener
BiobaseBlast900.0BLAST-related tools (bioinformatics, gpl, library)2017-09-28ChristianHoener
BiobaseDotP270.0Vienna / DotBracket / ExtSS parsers (bioinformatics, gpl, library)2011-08-22ChristianHoener
BiobaseEnsembl380.0Ensembl related datastructures and functions (bioinformatics, gpl, library)2018-12-12FlorianEggenhofer
BiobaseFR3D850.0Importer for FR3D resources (bioinformatics, gpl, library)2012-02-16ChristianHoener
BiobaseFasta1560.0streaming FASTA parser (bioinformatics, gpl, library)2018-12-12ChristianHoener
BiobaseHTTP360.0Libary to interface with the Bioinformatics HTTP services - Entrez Ensembl (bioinformatics, gpl, library)2018-12-12FlorianEggenhofer
BiobaseHTTPTools330.0Tools to query Bioinformatics HTTP services e.g. Entrez, Ensembl. (bioinformatics, gpl, program)2018-12-13FlorianEggenhofer
BiobaseInfernal3860.0Infernal data structures and tools (bioinformatics, gpl, library, program)2017-03-14ChristianHoener
BiobaseMAF280.0Multiple Alignment Format (bioinformatics, gpl, library)2011-07-29ChristianHoener
BiobaseNewick660.0Newick file format parser. (bioinformatics, bsd3, library, program)2017-07-07ChristianHoener
BiobaseTrainingData900.0RNA folding training data (bioinformatics, gpl, library, program)2011-09-29ChristianHoener
BiobaseTurner1860.0Import Turner RNA parameters (bioinformatics, gpl, library)2013-04-25ChristianHoener
BiobaseTypes2200.0Collection of types for bioinformatics (bioinformatics, bsd3, data-structures, library)2018-12-11ChristianHoener
BiobaseVienna1650.0Import Vienna energy parameters (bioinformatics, gpl, library)2013-04-22ChristianHoener
BiobaseXNA5030.0Efficient RNA/DNA/Protein Primary/Secondary Structure (bioinformatics, gpl, library, program)2017-11-23ChristianHoener
BlastHTTP1690.0Libary to interface with the NCBI blast REST interface (bioinformatics, gpl, library)2018-03-12FlorianEggenhofer
CMCompare790.0Infernal covariance model comparison (bioinformatics, gpl, library, program)2012-11-22ChristianHoener
ClustalParser3350.0Libary for parsing Clustal tools output (bioinformatics, gpl, library, program)2018-03-12FlorianEggenhofer
DnaProteinAlignment360.0Frameshift-aware alignment of protein sequences with DNA sequences (bioinformatics, gpl, library, program)2013-12-18ChristianHoener
EntrezHTTP (deprecated in favor of BiobaseHTTP)990.0Libary to interface with the NCBI Entrez REST service. (bioinformatics, deprecated, gpl, library)2017-08-10FlorianEggenhofer
ForestStructures980.0Tree- and forest structures (bioinformatics, bsd3, formal-languages, library)2018-12-11ChristianHoener
Forestry260.0Comparison of trees and forests. (bioinformatics, bsd3, formal-languages, library)2017-11-23ChristianHoener
FormalGrammars2440.0(Context-free) grammars in formal language theory (bioinformatics, formal-languages, gpl, library, program)2017-08-31ChristianHoener
Genbank1270.0Libary for processing the NCBI genbank format (bioinformatics, library, program)2014-10-26FlorianEggenhofer
Gene-CluEDO660.0Hox gene clustering (bioinformatics, gpl, library, program)2017-09-11ChristianHoener
GenussFold390.0MCFGs for Genus-1 RNA Pseudoknots (bioinformatics, formal-languages, gpl, library, program)2015-07-16ChristianHoener
GrammarProducts2140.0Grammar products and higher-dimensional grammars (bioinformatics, formal-languages, gpl, library)2017-03-14ChristianHoener
MC-Fold-DP590.0Folding algorithm based on nucleotide cyclic motifs. (bioinformatics, gpl, library, program)2012-11-12ChristianHoener
MutationOrder840.0Most likely order of mutation events in RNA (bioinformatics, gpl, library, program)2017-10-24ChristianHoener
Nussinov78940.0Nussinov78 using the ADPfusion library. (bioinformatics, gpl, library, program)2012-11-07ChristianHoener
PDBtools590.0A library for analysis of 3-D protein coordinates (bioinformatics, gpl, library)2012-06-03GrantRotskoff
RNAFold1130.0RNA secondary structure prediction (bioinformatics, gpl, library, program)2013-12-06ChristianHoener
RNAFoldProgs530.0RNA secondary structure folding (bioinformatics, gpl, program)2010-09-23ChristianHoener
RNAdesign900.0Multi-target RNA sequence design (bioinformatics, gpl, library, program)2014-02-13ChristianHoener
RNAdraw270.0Draw RNA secondary structures (bioinformatics, gpl, library, program)2014-02-03ChristianHoener
RNAlien3122.0Unsupervized construction of RNA family models (bioinformatics, gpl, library, program)2017-03-13FlorianEggenhofer
RNAwolf1030.0RNA folding with non-canonical basepairs and base-triplets. (bioinformatics, gpl, library, program)2011-09-29ChristianHoener
SelectSequencesFromMSA1080.0Selects a representative subset of sequences from multiple sequence alignment. (bioinformatics, gpl, library, program)2018-03-12FlorianEggenhofer
StockholmAlignment2142.0Libary for Stockholm aligmnent format (bioinformatics, gpl, library)2018-01-15FlorianEggenhofer
Taxonomy700.0Libary for parsing, processing and vizualization of taxonomy data (bioinformatics, gpl, library)2017-08-10FlorianEggenhofer
TaxonomyTools620.0Tool for parsing, processing, comparing and visualizing taxonomy data (bioinformatics, gpl, program)2017-01-26FlorianEggenhofer
ViennaRNA-bindings1800.0ViennaRNA v2 bindings (bindings, bioinformatics, ffi, library)2017-11-23ChristianHoener
ViennaRNA-extras270.0ViennaRNA v2 extensions (bioinformatics, bsd3, library)2017-11-23ChristianHoener
ViennaRNAParser3880.0Libary for parsing ViennaRNA package output (bioinformatics, gpl, library)2017-10-18FlorianEggenhofer
a50900.0Compare genome assemblies (bioinformatics, program)2013-07-23KetilMalde
adp-multi1120.0ADP for multiple context-free languages (algorithms, bioinformatics, bsd3, data-structures, library)2013-05-29MaikRiechert
adp-multi-monadiccp550.0Subword construction in adp-multi using monadiccp (algorithms, bioinformatics, bsd3, data-structures, library)2013-05-29MaikRiechert
bamstats720.0A program to extract various information from BAM alignmnet files. (bioinformatics, library, program)2013-10-18KetilMalde
bio2690.0A bioinformatics library (bioinformatics, library)2013-07-20GwernBranwen, KetilMalde
bioace540.0Library for reading ace assembly files (bioinformatics, library)2012-06-19DanFornika
bioalign1670.0Data structures and helper functions for calculating alignments (bioinformatics, library)2012-06-19DanFornika
biocore1310.0A bioinformatics library (bioinformatics, library)2013-01-07KetilMalde
biofasta1040.0Library for reading fasta sequence files (bioinformatics, library)2013-01-10DanFornika
biofastq370.0A library for reading FASTQ files (bioinformatics, library)2012-10-23KetilMalde
biohazard4580.0bioinformatics support library (bioinformatics, bsd3, library)2018-10-15ustenzel
biophd1470.0Library for reading phd sequence files (bioinformatics, library)2015-05-20DanFornika
biopsl1120.0Library and executables for working with PSL files (bioinformatics, library, program)2012-11-19KetilMalde
biosff2290.0Library and executables for working with SFF files (bioinformatics, lgpl, library)2013-09-28KetilMalde
biostockholm1650.0Parsing and rendering of Stockholm files (used by Pfam, Rfam and Infernal). (bioinformatics, bsd3, library)2015-07-21FelipeLessa
birch-beer590.0Plot a colorful tree. (bioinformatics, gpl, library, program)2019-01-21GregorySchwartz
blastxml1200.0Library for reading Blast XML output (bioinformatics, library)2014-10-29KetilMalde
blosum1150.0BLOSUM generator (bioinformatics, gpl, library, program)2016-11-30GregorySchwartz
classify-frog600.0Classify sounds produced by Xenopus laevis (bioinformatics, bsd3, program)2019-01-05HenningThielemann
clustertools760.0Tools for manipulating sequence clusters (bioinformatics, program)2011-06-06GwernBranwen, KetilMalde
cmv1961.5Detailed visualization of CMs, HMMs and their comparisions (bioinformatics, gpl, library, program)2018-01-28FlorianEggenhofer
collapse-duplication320.0Collapse the duplication output into clones and return their frequencies. (bioinformatics, gpl, library, program)2018-08-28GregorySchwartz
convert-annotation1500.0Convert the annotation of a gene to another in a delimited file using a variety of different databases. (bioinformatics, gpl, library, program)2018-02-07GregorySchwartz
dephd1080.0Analyze quality of nucleotide sequences. (bioinformatics, program)2011-03-21GwernBranwen, KetilMalde
differential340.0Finds out whether an entity comes from different distributions (statuses). (bioinformatics, gpl, library, program)2019-01-10GregorySchwartz
diversity5820.0Quantify the diversity of a population (bioinformatics, gpl, library, program)2017-09-01GregorySchwartz
estreps460.0Repeats from ESTs (bioinformatics, program)2009-10-07GwernBranwen, KetilMalde
flower1500.0Analyze 454 flowgrams (.SFF files) (bioinformatics, program)2013-09-19KetilMalde
flowsim940.0Simulate 454 pyrosequencing (bioinformatics, gpl, program)2013-11-19KetilMalde
gact380.0General Alignment Clustering Tool (bioinformatics, program)2012-03-26KetilMalde
hPDB4522.0Protein Databank file format library (bioinformatics, bsd3, library)2018-07-14MichalGajda
hPDB-examples2750.0Examples for hPDB library (bioinformatics, bsd3, program)2018-07-14MichalGajda
hTalos240.0Parser, print and manipulate structures in PDB file format. (bioinformatics, bsd3, library)2013-11-23MichalGajda
heatitup290.0Find and annotate ITDs. (bioinformatics, gpl, library, program)2018-08-28GregorySchwartz
heatitup-complete280.0Find and annotate ITDs with assembly or read pair joining. (bioinformatics, gpl, library, program)2018-08-28GregorySchwartz
hemokit1340.0Haskell port of the Emokit EEG project (bioinformatics, library, mit, program)2015-08-19NiklasHambuechen, PatrickChilton
hierarchical-spectral-clustering1730.0Hierarchical spectral clustering of a graph. (bioinformatics, gpl, library, program)2019-03-01GregorySchwartz
hyraxAbif800.0Modules for parsing, generating and manipulating AB1 files. (ab1, abif, bioinformatics, chromatogram, library, program)2019-01-10andrevdm
integreat230.0Integrate different assays. (bioinformatics, gpl, library, program)2018-05-16GregorySchwartz
korfu340.0The Korfu ORF Utility (bioinformatics, program)2010-09-10KetilMalde
memexml380.0Library for reading Meme XML output (bioinformatics, bsd3, library)2015-09-11FlorianEggenhofer
mmtf540.0Macromolecular Transmission Format implementation (bioinformatics, bsd3, library)2019-02-10zmactep
modify-fasta2200.0Modify fasta (and CLIP) files in several optional ways (bioinformatics, gpl, library, program)2018-04-02GregorySchwartz
modularity890.0Find the modularity of a network. (bioinformatics, gpl, library)2019-01-24GregorySchwartz
normalize740.0Normalize data using a variety of methods. (bioinformatics, gpl, library, program)2018-06-29GregorySchwartz
phybin590.0Utility for clustering phylogenetic trees in Newick format based on Robinson-Foulds distance. (bioinformatics, bsd3, library, program)2013-09-20RyanNewton
pipes-ordered-zip240.0merge two ordered Producers into a new Producer (bioinformatics, bsd3, library)2019-03-05stephan_schiffels
rank-product1430.0Find the rank product of a data set. (bioinformatics, gpl, library, program)2018-09-12GregorySchwartz
rbr220.0Mask nucleotide (EST) sequences in Fasta format (bioinformatics, program)2010-09-09GwernBranwen, KetilMalde
samtools700.0Binding to the C samtools library (bioinformatics, library, mit)2016-05-30NicholasIngolia
samtools-conduit220.0Conduit interface to SAM/BAM format files through samtools (bioinformatics, library, mit, program)2014-11-29NicholasIngolia
samtools-enumerator240.0Enumerator interface to SamTools library (bioinformatics, library, mit)2012-01-21NicholasIngolia
samtools-iteratee310.0Iteratee interface to SamTools library (bioinformatics, library, mit)2014-01-24NicholasIngolia
seqloc1970.0Handle sequence locations for bioinformatics (bioinformatics, library, mit)2015-01-16NicholasIngolia
seqloc-datafiles520.0Read and write BED and GTF format genome annotations (bioinformatics, library, mit, program)2015-03-20NicholasIngolia
sequence-formats230.0A package with basic parsing utilities for several Bioinformatic data formats. (bioinformatics, gpl, library)2019-03-05stephan_schiffels
sgrep150.0Sgrep - grep Fasta files for sequences matching a regular expression (bioinformatics, program)2010-09-13KetilMalde
simseq120.0Simulate sequencing with different models for priming and errors (bioinformatics, program)2008-03-08GwernBranwen
smiles630.0 (bioinformatics, bsd3, library)2017-08-15fonturacetamum
subsample140.0Subsample data. (bioinformatics, gpl, library, program)2018-05-16GregorySchwartz
too-many-cells1220.0Cluster single cells and analyze cell clade relationships. (bioinformatics, gpl, library, program)2019-03-06GregorySchwartz
trimpolya100.0Search for, annotate and trim poly-A tail (bioinformatics, program)2009-12-15KetilMalde
varan240.0Process mpileup output to identify significant differences (bioinformatics, program)2014-12-01KetilMalde
vcf162.0A package to parse VCF files inspired in similar python libraries (bioinformatics, library, mit)2017-08-10juanpaucar
xml2x320.0Convert BLAST output in XML format to CSV or HTML (bioinformatics, program)2009-10-07GwernBranwen, KetilMalde
xsact170.0Cluster EST sequences (bioinformatics, program)2010-09-09GwernBranwen, KetilMalde
zsyntax130.0Automated theorem prover for the Zsyntax biochemical calculus (bioinformatics, bsd3, library, logic, theorem-provers)2018-12-15fsestini