Packages tagged bioinformatics

126 packages have this tag.

[Merge tag] (trustees only)

Related tags: library (106), program (69), gpl (68), bsd3 (21), mit (9), formal-languages (8), data-structures (6), algorithms (5), ab1 (1), abif (1), bindings (1), chromatogram (1), ...

Name
DLs
Rating
Rev Deps
Description
Tags
Last U/L
Last Version
Maintainers
ADPfusion540.015Efficient, high-level dynamic programming. (algorithms, bioinformatics, bsd3, data-structures, formal-languages, library)2019-10-010.6.0.0ChristianHoener
ADPfusionForest60.01Dynamic programming on tree and forest structures (bioinformatics, bsd3, formal-languages, library)2017-11-230.0.0.1ChristianHoener
ADPfusionSet130.03Dynamic programming for Set data structures. (algorithms, bioinformatics, bsd3, data-structures, formal-languages, library)2017-10-190.0.0.2ChristianHoener
AlignmentAlgorithms150.01Collection of alignment algorithms (algorithms, bioinformatics, data-structures, gpl, library, linguistics)2017-03-140.1.0.0ChristianHoener
BCMtools150.00Big Contact Map Tools (bioinformatics, library, mit, program)2015-05-050.1.1kaizhang
BioHMM700.01Libary for Hidden Markov Models in HMMER3 format. (bioinformatics, gpl, library)2017-06-091.2.0FlorianEggenhofer
Biobase220.06Base library for bioinformatics (bioinformatics, gpl, library)2011-04-080.3.1.1ChristianHoener
BiobaseBlast250.04BLAST-related tools (bioinformatics, gpl, library)2021-06-050.3.3.0ChristianHoener, FlorianEggenhofer
BiobaseDotP70.02Vienna / DotBracket / ExtSS parsers (bioinformatics, gpl, library)2011-08-220.1.0.0ChristianHoener
BiobaseEnsembl210.01Ensembl related datastructures and functions (bioinformatics, gpl, library)2020-01-090.2.0.1FlorianEggenhofer
BiobaseFR3D140.02Importer for FR3D resources (bioinformatics, gpl, library)2012-02-160.2.3.0ChristianHoener
BiobaseFasta350.04streaming FASTA parser (bioinformatics, bsd3, library, program)2021-06-040.4.0.1ChristianHoener
BiobaseHTTP80.01Libary to interface with the Bioinformatics HTTP services - Entrez Ensembl (bioinformatics, gpl, library)2019-11-201.2.0FlorianEggenhofer
BiobaseHTTPTools90.00Tools to query Bioinformatics HTTP services e.g. Entrez, Ensembl. (bioinformatics, gpl, program)2018-12-131.0.0FlorianEggenhofer
BiobaseInfernal400.03Infernal data structures and tools (bioinformatics, gpl, library, program)2017-03-140.8.1.0ChristianHoener
BiobaseMAF60.01Multiple Alignment Format (bioinformatics, gpl, library)2011-07-290.5.0.0ChristianHoener
BiobaseNewick120.02Newick file format parser. (bioinformatics, bsd3, library, program)2017-07-070.0.0.2ChristianHoener
BiobaseTrainingData150.02RNA folding training data (bioinformatics, gpl, library, program)2011-09-290.1.2.3ChristianHoener
BiobaseTurner380.04Import Turner RNA parameters (bioinformatics, gpl, library)2013-04-250.3.1.1ChristianHoener
BiobaseTypes450.012Collection of types for bioinformatics (bioinformatics, bsd3, data-structures, library)2021-06-040.2.1.0ChristianHoener
BiobaseVienna270.03Import Vienna energy parameters (bioinformatics, gpl, library)2013-04-220.3.0.0ChristianHoener
BiobaseXNA840.017Efficient RNA/DNA/Protein Primary/Secondary Structure (bioinformatics, bsd3, library, program)2021-06-040.11.1.1ChristianHoener
BlastHTTP410.02Libary to interface with the NCBI blast REST interface (bioinformatics, gpl, library)2021-06-051.4.2FlorianEggenhofer
CMCompare170.01Infernal covariance model comparison (bioinformatics, gpl, library, program)2012-11-220.0.1.5ChristianHoener
ClustalParser630.03Libary for parsing Clustal tools output (bioinformatics, gpl, library, program)2019-11-141.3.0FlorianEggenhofer
DnaProteinAlignment50.01Frameshift-aware alignment of protein sequences with DNA sequences (bioinformatics, gpl, library, program)2013-12-180.0.0.1ChristianHoener
EntrezHTTP (deprecated in favor of BiobaseHTTP)170.01Libary to interface with the NCBI Entrez REST service. (bioinformatics, deprecated, gpl, library)2017-08-101.0.4FlorianEggenhofer
ForestStructures320.05Tree- and forest structures (bioinformatics, bsd3, formal-languages, library)2018-12-110.0.1.0ChristianHoener
Forestry80.01Comparison of trees and forests. (bioinformatics, bsd3, formal-languages, library)2017-11-230.0.0.1ChristianHoener
FormalGrammars320.09(Context-free) grammars in formal language theory (bioinformatics, formal-languages, gpl, library)2019-10-020.4.0.0ChristianHoener
Genbank170.01Libary for processing the NCBI genbank format (bioinformatics, library, program)2014-10-261.0.3FlorianEggenhofer
Gene-CluEDO80.00Hox gene clustering (bioinformatics, gpl, library, program)2017-09-110.0.0.2ChristianHoener
GenussFold80.00MCFGs for Genus-1 RNA Pseudoknots (bioinformatics, formal-languages, gpl, library, program)2015-07-160.0.0.2ChristianHoener
GrammarProducts250.04Grammar products and higher-dimensional grammars (bioinformatics, formal-languages, gpl, library)2019-10-020.2.0.0ChristianHoener
MC-Fold-DP130.01Folding algorithm based on nucleotide cyclic motifs. (bioinformatics, gpl, library, program)2012-11-120.1.1.0ChristianHoener
MutationOrder110.00Most likely order of mutation events in RNA (bioinformatics, gpl, library, program)2017-10-240.0.1.0ChristianHoener
Nussinov78200.01Nussinov78 using the ADPfusion library. (bioinformatics, gpl, library, program)2012-11-070.1.0.0ChristianHoener
PDBtools120.01A library for analysis of 3-D protein coordinates (bioinformatics, gpl, library)2012-06-030.0.3GrantRotskoff
RNAFold220.02RNA secondary structure prediction (bioinformatics, gpl, library, program)2013-12-061.99.3.4ChristianHoener
RNAFoldProgs100.01RNA secondary structure folding (bioinformatics, gpl, program)2010-09-230.0.0.3ChristianHoener
RNAdesign190.01Multi-target RNA sequence design (bioinformatics, gpl, library, program)2014-02-130.1.2.2ChristianHoener
RNAdraw60.01Draw RNA secondary structures (bioinformatics, gpl, library, program)2014-02-030.2.0.1ChristianHoener
RNAlien322.00Unsupervized construction of RNA family models (bioinformatics, gpl, library, program)2019-08-291.7.0FlorianEggenhofer
RNAwolf150.01RNA folding with non-canonical basepairs and base-triplets. (bioinformatics, gpl, library, program)2011-09-290.4.0.0ChristianHoener
SelectSequencesFromMSA120.00Selects a representative subset of sequences from multiple sequence alignment. (bioinformatics, gpl, library, program)2018-03-121.0.5FlorianEggenhofer
StockholmAlignment302.02Libary for Stockholm aligmnent format (bioinformatics, gpl, library)2019-12-171.3.0FlorianEggenhofer
Taxonomy250.03Libary for parsing, processing and vizualization of taxonomy data (bioinformatics, gpl, library)2021-05-302.2.0FlorianEggenhofer
TaxonomyTools70.01Tool for parsing, processing, comparing and visualizing taxonomy data (bioinformatics, gpl, program)2017-01-261.0.1FlorianEggenhofer
ViennaRNA-bindings310.04ViennaRNA v2 bindings (bindings, bioinformatics, ffi, library)2017-11-230.233.2.0ChristianHoener
ViennaRNA-extras100.01ViennaRNA v2 extensions (bioinformatics, bsd3, library)2017-11-230.0.0.1ChristianHoener
ViennaRNAParser690.03Libary for parsing ViennaRNA package output (bioinformatics, gpl, library)2017-10-181.3.3FlorianEggenhofer
a50160.01Compare genome assemblies (bioinformatics, program)2013-07-230.5KetilMalde
adp-multi210.02ADP for multiple context-free languages (algorithms, bioinformatics, bsd3, data-structures, library)2013-05-290.2.3MaikRiechert
adp-multi-monadiccp80.01Subword construction in adp-multi using monadiccp (algorithms, bioinformatics, bsd3, data-structures, library)2013-05-290.2.1MaikRiechert
bamstats180.01A program to extract various information from BAM alignmnet files. (bioinformatics, library, program)2013-10-180.4KetilMalde
bio470.02A bioinformatics library (bioinformatics, library)2013-07-200.5.3GwernBranwen, KetilMalde
bioace180.01Library for reading ace assembly files (bioinformatics, library)2012-06-190.0.1DanFornika
bioalign260.02Data structures and helper functions for calculating alignments (bioinformatics, library)2012-06-190.0.5DanFornika
biocore270.020A bioinformatics library (bioinformatics, library)2013-01-070.3.1KetilMalde
biofasta210.05Library for reading fasta sequence files (bioinformatics, library)2013-01-100.0.3DanFornika
biofastq170.01A library for reading FASTQ files (bioinformatics, library)2012-10-230.1KetilMalde
biohazard460.01bioinformatics support library (bioinformatics, bsd3, library)2020-01-062.1ustenzel
biophd380.01Library for reading phd sequence files (bioinformatics, library)2015-05-200.0.8DanFornika
biopsl200.01Library and executables for working with PSL files (bioinformatics, library, program)2012-11-190.4KetilMalde
biosff340.01Library and executables for working with SFF files (bioinformatics, lgpl, library)2013-09-280.3.7.1KetilMalde
biostockholm230.01Parsing and rendering of Stockholm files (used by Pfam, Rfam and Infernal). (bioinformatics, bsd3, library)2015-07-210.3.4FelipeLessa
birch-beer530.01Plot a colorful tree. (bioinformatics, gpl, library, program)2022-10-060.4.2.1GregorySchwartz
blastxml260.03Library for reading Blast XML output (bioinformatics, library)2014-10-290.3.2KetilMalde
blosum120.00BLOSUM generator (bioinformatics, gpl, library, program)2016-11-300.1.1.4GregorySchwartz
classify-frog160.01Classify sounds produced by Xenopus laevis (bioinformatics, bsd3, program)2019-08-130.2.4.3HenningThielemann
clustertools130.01Tools for manipulating sequence clusters (bioinformatics, program)2011-06-060.1.5GwernBranwen, KetilMalde
cmv221.50Detailed visualization of CMs, HMMs and their comparisions (bioinformatics, gpl, library, program)2018-01-281.0.8FlorianEggenhofer
collapse-duplication70.00Collapse the duplication output into clones and return their frequencies. (bioinformatics, gpl, library, program)2018-08-280.4.0.1GregorySchwartz
convert-annotation210.00Convert the annotation of a gene to another in a delimited file using a variety of different databases. (bioinformatics, gpl, library, program)2018-02-070.5.1.0GregorySchwartz
dephd170.01Analyze quality of nucleotide sequences. (bioinformatics, program)2011-03-210.1.6GwernBranwen, KetilMalde
differential120.01Finds out whether an entity comes from different distributions (statuses). (bioinformatics, gpl, library, program)2021-02-050.2.0.1GregorySchwartz
diversity880.03Quantify the diversity of a population (bioinformatics, gpl, library, program)2017-09-010.8.1.0GregorySchwartz
elynx670.00Validate and (optionally) redo ELynx analyses (bioinformatics, gpl, program)2023-01-140.7.0.1dschrempf
elynx-markov730.01Simulate molecular sequences along trees (bioinformatics, gpl, library)2023-01-140.7.0.1dschrempf
elynx-nexus770.01Import and export Nexus files (bioinformatics, gpl, library)2023-01-140.7.0.1dschrempf
elynx-seq870.03Handle molecular sequences (bioinformatics, gpl, library)2023-01-140.7.0.1dschrempf
elynx-tools850.05Tools for ELynx (bioinformatics, gpl, library)2023-01-140.7.0.1dschrempf
elynx-tree770.04Handle phylogenetic trees (bioinformatics, gpl, library)2023-01-140.7.0.1dschrempf
estreps60.01Repeats from ESTs (bioinformatics, program)2009-10-070.3.1GwernBranwen, KetilMalde
flower220.01Analyze 454 flowgrams (.SFF files) (bioinformatics, program)2013-09-190.7.2KetilMalde
flowsim100.01Simulate 454 pyrosequencing (bioinformatics, gpl, program)2013-11-190.3.5KetilMalde
gact60.01General Alignment Clustering Tool (bioinformatics, program)2012-03-260.2KetilMalde
heatitup40.00Find and annotate ITDs. (bioinformatics, gpl, library, program)2019-06-130.5.4.0GregorySchwartz
heatitup-complete70.00Find and annotate ITDs with assembly or read pair joining. (bioinformatics, gpl, library, program)2020-02-170.5.5.0GregorySchwartz
hemokit170.01Haskell port of the Emokit EEG project (bioinformatics, library, mit, program)2015-08-190.6.6NiklasHambuechen, PatrickChilton
hierarchical-spectral-clustering70.02Hierarchical spectral clustering of a graph. (bioinformatics, gpl, library, program)2019-09-260.5.0.1GregorySchwartz
hyraxAbif500.01Modules for parsing, generating and manipulating AB1 files. (ab1, abif, bioinformatics, chromatogram, library, program)2023-01-170.2.3.27andrevdm
integreat90.00Integrate different assays. (bioinformatics, gpl, library, program)2018-05-160.2.2.1GregorySchwartz
korfu50.01The Korfu ORF Utility (bioinformatics, program)2010-09-100.2KetilMalde
memexml80.01Library for reading Meme XML output (bioinformatics, bsd3, library)2015-09-110.0.3FlorianEggenhofer
mmtf90.01Macromolecular Transmission Format implementation (bioinformatics, bsd3, library)2019-02-100.1.3.1zmactep
modify-fasta200.00Modify fasta (and CLIP) files in several optional ways (bioinformatics, gpl, library, program)2018-04-020.8.3.0GregorySchwartz
modularity90.02Find the modularity of a network. (bioinformatics, gpl, library)2019-08-080.2.1.1GregorySchwartz
normalize170.00Normalize data using a variety of methods. (bioinformatics, gpl, library, program)2018-06-290.3.1.1GregorySchwartz
phybin180.01Utility for clustering phylogenetic trees in Newick format based on Robinson-Foulds distance. (bioinformatics, bsd3, library, program)2013-09-200.3RyanNewton
pipes-ordered-zip260.00merge two ordered Producers into a new Producer (bioinformatics, bsd3, library)2021-02-251.2.1stephan_schiffels
ploterific100.01Basic plotting of tabular data for the command line. (bioinformatics, gpl, library, program)2022-04-140.2.1.4GregorySchwartz
rank-product160.02Find the rank product of a data set. (bioinformatics, gpl, library, program)2018-09-120.2.2.0GregorySchwartz
rbr80.01Mask nucleotide (EST) sequences in Fasta format (bioinformatics, program)2010-09-090.8.6GwernBranwen, KetilMalde
samtools270.05Binding to the C samtools library (bioinformatics, library, mit)2016-05-300.2.4.3NicholasIngolia
samtools-conduit80.01Conduit interface to SAM/BAM format files through samtools (bioinformatics, library, mit, program)2014-11-290.1.1.0NicholasIngolia
samtools-enumerator140.01Enumerator interface to SamTools library (bioinformatics, library, mit)2012-01-210.1.2.1NicholasIngolia
samtools-iteratee90.01Iteratee interface to SamTools library (bioinformatics, library, mit)2014-01-240.2.2.1NicholasIngolia
seqloc280.03Handle sequence locations for bioinformatics (bioinformatics, library, mit)2015-01-160.6.1.1NicholasIngolia
seqloc-datafiles220.01Read and write BED and GTF format genome annotations (bioinformatics, library, mit, program)2015-03-200.4.2NicholasIngolia
sequence-formats420.01A package with basic parsing utilities for several Bioinformatic data formats. (bioinformatics, gpl, library)2022-03-301.6.6.1stephan_schiffels
sequenceTools170.00A package with tools for processing DNA sequencing data (bioinformatics, gpl, library, program)2022-02-171.5.2stephan_schiffels
sgrep70.01Sgrep - grep Fasta files for sequences matching a regular expression (bioinformatics, program)2010-09-130.0KetilMalde
simseq60.01Simulate sequencing with different models for priming and errors (bioinformatics, program)2008-03-080.0GwernBranwen
slynx800.00Handle molecular sequences (bioinformatics, gpl, library, program)2023-01-140.7.0.1dschrempf
smiles100.01 (bioinformatics, bsd3, library)2017-08-150.2.0.0fonturacetamum
subsample110.00Subsample data. (bioinformatics, gpl, library, program)2018-05-160.1.0.0GregorySchwartz
tex-join-bib40.00Compile separate tex files with the same bibliography. (bioinformatics, gpl, library, program)2020-03-120.1.0.0GregorySchwartz
tlynx820.00Handle phylogenetic trees (bioinformatics, gpl, library, program)2023-01-140.7.0.1dschrempf
too-many-cells380.00Cluster single cells and analyze cell clade relationships. (bioinformatics, gpl, library, program)2022-10-063.0.1.0GregorySchwartz
trimpolya40.01Search for, annotate and trim poly-A tail (bioinformatics, program)2009-12-150KetilMalde
varan90.01Process mpileup output to identify significant differences (bioinformatics, program)2014-12-010.5.1KetilMalde
vcf52.01A package to parse VCF files inspired in similar python libraries (bioinformatics, library, mit)2017-08-100.9.0juanpaucar
xml2x160.01Convert BLAST output in XML format to CSV or HTML (bioinformatics, program)2009-10-070.4.2GwernBranwen, KetilMalde
xsact130.01Cluster EST sequences (bioinformatics, program)2010-09-091.7.3GwernBranwen, KetilMalde
zsyntax50.00Automated theorem prover for the Zsyntax biochemical calculus (bioinformatics, bsd3, library, logic, theorem-provers)2018-12-150.2.0.0fsestini