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
Description
Tags
Last U/L
Maintainer
ADPfusion900.0Efficient, high-level dynamic programming. (algorithms, bioinformatics, bsd3, data-structures, formal-languages, library)2019-10-01ChristianHoener
ADPfusionForest80.0Dynamic programming on tree and forest structures (bioinformatics, bsd3, formal-languages, library)2017-11-23ChristianHoener
ADPfusionSet150.0Dynamic programming for Set data structures. (algorithms, bioinformatics, bsd3, data-structures, formal-languages, library)2017-10-19ChristianHoener
AlignmentAlgorithms250.0Collection of alignment algorithms (algorithms, bioinformatics, data-structures, gpl, library, linguistics)2017-03-14ChristianHoener
BCMtools110.0Big Contact Map Tools (bioinformatics, library, mit, program)2015-05-05kaizhang
BioHMM640.0Libary for Hidden Markov Models in HMMER3 format. (bioinformatics, gpl, library)2017-06-09FlorianEggenhofer
Biobase160.0Base library for bioinformatics (bioinformatics, gpl, library)2011-04-08ChristianHoener
BiobaseBlast260.0BLAST-related tools (bioinformatics, gpl, library)2021-06-05ChristianHoener, FlorianEggenhofer
BiobaseDotP80.0Vienna / DotBracket / ExtSS parsers (bioinformatics, gpl, library)2011-08-22ChristianHoener
BiobaseEnsembl190.0Ensembl related datastructures and functions (bioinformatics, gpl, library)2020-01-09FlorianEggenhofer
BiobaseFR3D180.0Importer for FR3D resources (bioinformatics, gpl, library)2012-02-16ChristianHoener
BiobaseFasta280.0streaming FASTA parser (bioinformatics, bsd3, library, program)2021-06-04ChristianHoener
BiobaseHTTP60.0Libary to interface with the Bioinformatics HTTP services - Entrez Ensembl (bioinformatics, gpl, library)2019-11-20FlorianEggenhofer
BiobaseHTTPTools60.0Tools to query Bioinformatics HTTP services e.g. Entrez, Ensembl. (bioinformatics, gpl, program)2018-12-13FlorianEggenhofer
BiobaseInfernal550.0Infernal data structures and tools (bioinformatics, gpl, library, program)2017-03-14ChristianHoener
BiobaseMAF80.0Multiple Alignment Format (bioinformatics, gpl, library)2011-07-29ChristianHoener
BiobaseNewick60.0Newick file format parser. (bioinformatics, bsd3, library, program)2017-07-07ChristianHoener
BiobaseTrainingData170.0RNA folding training data (bioinformatics, gpl, library, program)2011-09-29ChristianHoener
BiobaseTurner500.0Import Turner RNA parameters (bioinformatics, gpl, library)2013-04-25ChristianHoener
BiobaseTypes480.0Collection of types for bioinformatics (bioinformatics, bsd3, data-structures, library)2021-06-04ChristianHoener
BiobaseVienna330.0Import Vienna energy parameters (bioinformatics, gpl, library)2013-04-22ChristianHoener
BiobaseXNA1120.0Efficient RNA/DNA/Protein Primary/Secondary Structure (bioinformatics, bsd3, library, program)2021-06-04ChristianHoener
BlastHTTP350.0Libary to interface with the NCBI blast REST interface (bioinformatics, gpl, library)2021-06-05FlorianEggenhofer
CMCompare30.0Infernal covariance model comparison (bioinformatics, gpl, library, program)2012-11-22ChristianHoener
ClustalParser410.0Libary for parsing Clustal tools output (bioinformatics, gpl, library, program)2019-11-14FlorianEggenhofer
DnaProteinAlignment40.0Frameshift-aware alignment of protein sequences with DNA sequences (bioinformatics, gpl, library, program)2013-12-18ChristianHoener
EntrezHTTP (deprecated in favor of BiobaseHTTP)150.0Libary to interface with the NCBI Entrez REST service. (bioinformatics, deprecated, gpl, library)2017-08-10FlorianEggenhofer
ForestStructures180.0Tree- and forest structures (bioinformatics, bsd3, formal-languages, library)2018-12-11ChristianHoener
Forestry60.0Comparison of trees and forests. (bioinformatics, bsd3, formal-languages, library)2017-11-23ChristianHoener
FormalGrammars310.0(Context-free) grammars in formal language theory (bioinformatics, formal-languages, gpl, library)2019-10-02ChristianHoener
Genbank90.0Libary for processing the NCBI genbank format (bioinformatics, library, program)2014-10-26FlorianEggenhofer
Gene-CluEDO110.0Hox gene clustering (bioinformatics, gpl, library, program)2017-09-11ChristianHoener
GenussFold50.0MCFGs for Genus-1 RNA Pseudoknots (bioinformatics, formal-languages, gpl, library, program)2015-07-16ChristianHoener
GrammarProducts130.0Grammar products and higher-dimensional grammars (bioinformatics, formal-languages, gpl, library)2019-10-02ChristianHoener
MC-Fold-DP70.0Folding algorithm based on nucleotide cyclic motifs. (bioinformatics, gpl, library, program)2012-11-12ChristianHoener
MutationOrder140.0Most likely order of mutation events in RNA (bioinformatics, gpl, library, program)2017-10-24ChristianHoener
Nussinov78110.0Nussinov78 using the ADPfusion library. (bioinformatics, gpl, library, program)2012-11-07ChristianHoener
PDBtools120.0A library for analysis of 3-D protein coordinates (bioinformatics, gpl, library)2012-06-03GrantRotskoff
RNAFold260.0RNA secondary structure prediction (bioinformatics, gpl, library, program)2013-12-06ChristianHoener
RNAFoldProgs100.0RNA secondary structure folding (bioinformatics, gpl, program)2010-09-23ChristianHoener
RNAdesign150.0Multi-target RNA sequence design (bioinformatics, gpl, library, program)2014-02-13ChristianHoener
RNAdraw30.0Draw RNA secondary structures (bioinformatics, gpl, library, program)2014-02-03ChristianHoener
RNAlien302.0Unsupervized construction of RNA family models (bioinformatics, gpl, library, program)2019-08-29FlorianEggenhofer
RNAwolf210.0RNA folding with non-canonical basepairs and base-triplets. (bioinformatics, gpl, library, program)2011-09-29ChristianHoener
SelectSequencesFromMSA100.0Selects a representative subset of sequences from multiple sequence alignment. (bioinformatics, gpl, library, program)2018-03-12FlorianEggenhofer
StockholmAlignment292.0Libary for Stockholm aligmnent format (bioinformatics, gpl, library)2019-12-17FlorianEggenhofer
Taxonomy180.0Libary for parsing, processing and vizualization of taxonomy data (bioinformatics, gpl, library)2021-05-30FlorianEggenhofer
TaxonomyTools90.0Tool for parsing, processing, comparing and visualizing taxonomy data (bioinformatics, gpl, program)2017-01-26FlorianEggenhofer
ViennaRNA-bindings390.0ViennaRNA v2 bindings (bindings, bioinformatics, ffi, library)2017-11-23ChristianHoener
ViennaRNA-extras60.0ViennaRNA v2 extensions (bioinformatics, bsd3, library)2017-11-23ChristianHoener
ViennaRNAParser360.0Libary for parsing ViennaRNA package output (bioinformatics, gpl, library)2017-10-18FlorianEggenhofer
a50140.0Compare genome assemblies (bioinformatics, program)2013-07-23KetilMalde
adp-multi160.0ADP for multiple context-free languages (algorithms, bioinformatics, bsd3, data-structures, library)2013-05-29MaikRiechert
adp-multi-monadiccp120.0Subword construction in adp-multi using monadiccp (algorithms, bioinformatics, bsd3, data-structures, library)2013-05-29MaikRiechert
bamstats150.0A program to extract various information from BAM alignmnet files. (bioinformatics, library, program)2013-10-18KetilMalde
bio180.0A bioinformatics library (bioinformatics, library)2013-07-20GwernBranwen, KetilMalde
bioace20.0Library for reading ace assembly files (bioinformatics, library)2012-06-19DanFornika
bioalign220.0Data structures and helper functions for calculating alignments (bioinformatics, library)2012-06-19DanFornika
biocore200.0A bioinformatics library (bioinformatics, library)2013-01-07KetilMalde
biofasta150.0Library for reading fasta sequence files (bioinformatics, library)2013-01-10DanFornika
biofastq70.0A library for reading FASTQ files (bioinformatics, library)2012-10-23KetilMalde
biohazard530.0bioinformatics support library (bioinformatics, bsd3, library)2020-01-06ustenzel
biophd210.0Library for reading phd sequence files (bioinformatics, library)2015-05-20DanFornika
biopsl10.0Library and executables for working with PSL files (bioinformatics, library, program)2012-11-19KetilMalde
biosff230.0Library and executables for working with SFF files (bioinformatics, lgpl, library)2013-09-28KetilMalde
biostockholm200.0Parsing 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)2021-04-16GregorySchwartz
blastxml150.0Library for reading Blast XML output (bioinformatics, library)2014-10-29KetilMalde
blosum110.0BLOSUM generator (bioinformatics, gpl, library, program)2016-11-30GregorySchwartz
classify-frog110.0Classify sounds produced by Xenopus laevis (bioinformatics, bsd3, program)2019-08-13HenningThielemann
clustertools110.0Tools for manipulating sequence clusters (bioinformatics, program)2011-06-06GwernBranwen, KetilMalde
cmv31.5Detailed visualization of CMs, HMMs and their comparisions (bioinformatics, gpl, library, program)2018-01-28FlorianEggenhofer
collapse-duplication50.0Collapse the duplication output into clones and return their frequencies. (bioinformatics, gpl, library, program)2018-08-28GregorySchwartz
convert-annotation170.0Convert the annotation of a gene to another in a delimited file using a variety of different databases. (bioinformatics, gpl, library, program)2018-02-07GregorySchwartz
dephd110.0Analyze quality of nucleotide sequences. (bioinformatics, program)2011-03-21GwernBranwen, KetilMalde
differential130.0Finds out whether an entity comes from different distributions (statuses). (bioinformatics, gpl, library, program)2021-02-05GregorySchwartz
diversity370.0Quantify the diversity of a population (bioinformatics, gpl, library, program)2017-09-01GregorySchwartz
elynx460.0Validate and (optionally) redo ELynx analyses (bioinformatics, gpl, program)2022-02-22dschrempf
elynx-markov230.0Simulate molecular sequences along trees (bioinformatics, gpl, library)2022-02-22dschrempf
elynx-nexus350.0Import and export Nexus files (bioinformatics, gpl, library)2022-02-22dschrempf
elynx-seq580.0Handle molecular sequences (bioinformatics, gpl, library)2022-02-22dschrempf
elynx-tools480.0Tools for ELynx (bioinformatics, gpl, library)2022-02-22dschrempf
elynx-tree570.0Handle phylogenetic trees (bioinformatics, gpl, library)2022-02-22dschrempf
estreps120.0Repeats from ESTs (bioinformatics, program)2009-10-07GwernBranwen, KetilMalde
flower270.0Analyze 454 flowgrams (.SFF files) (bioinformatics, program)2013-09-19KetilMalde
flowsim190.0Simulate 454 pyrosequencing (bioinformatics, gpl, program)2013-11-19KetilMalde
gact30.0General Alignment Clustering Tool (bioinformatics, program)2012-03-26KetilMalde
heatitup90.0Find and annotate ITDs. (bioinformatics, gpl, library, program)2019-06-13GregorySchwartz
heatitup-complete110.0Find and annotate ITDs with assembly or read pair joining. (bioinformatics, gpl, library, program)2020-02-17GregorySchwartz
hemokit260.0Haskell port of the Emokit EEG project (bioinformatics, library, mit, program)2015-08-19NiklasHambuechen, PatrickChilton
hierarchical-spectral-clustering70.0Hierarchical spectral clustering of a graph. (bioinformatics, gpl, library, program)2019-09-26GregorySchwartz
hyraxAbif390.0Modules for parsing, generating and manipulating AB1 files. (ab1, abif, bioinformatics, chromatogram, library, program)2020-11-18andrevdm
integreat60.0Integrate different assays. (bioinformatics, gpl, library, program)2018-05-16GregorySchwartz
korfu40.0The Korfu ORF Utility (bioinformatics, program)2010-09-10KetilMalde
memexml50.0Library for reading Meme XML output (bioinformatics, bsd3, library)2015-09-11FlorianEggenhofer
mmtf210.0Macromolecular Transmission Format implementation (bioinformatics, bsd3, library)2019-02-10zmactep
modify-fasta400.0Modify fasta (and CLIP) files in several optional ways (bioinformatics, gpl, library, program)2018-04-02GregorySchwartz
modularity210.0Find the modularity of a network. (bioinformatics, gpl, library)2019-08-08GregorySchwartz
normalize60.0Normalize data using a variety of methods. (bioinformatics, gpl, library, program)2018-06-29GregorySchwartz
phybin230.0Utility for clustering phylogenetic trees in Newick format based on Robinson-Foulds distance. (bioinformatics, bsd3, library, program)2013-09-20RyanNewton
pipes-ordered-zip160.0merge two ordered Producers into a new Producer (bioinformatics, bsd3, library)2021-02-25stephan_schiffels
ploterific290.0Basic plotting of tabular data for the command line. (bioinformatics, gpl, library, program)2022-04-14GregorySchwartz
rank-product240.0Find the rank product of a data set. (bioinformatics, gpl, library, program)2018-09-12GregorySchwartz
rbr10.0Mask nucleotide (EST) sequences in Fasta format (bioinformatics, program)2010-09-09GwernBranwen, KetilMalde
samtools460.0Binding to the C samtools library (bioinformatics, library, mit)2016-05-30NicholasIngolia
samtools-conduit70.0Conduit interface to SAM/BAM format files through samtools (bioinformatics, library, mit, program)2014-11-29NicholasIngolia
samtools-enumerator90.0Enumerator interface to SamTools library (bioinformatics, library, mit)2012-01-21NicholasIngolia
samtools-iteratee200.0Iteratee interface to SamTools library (bioinformatics, library, mit)2014-01-24NicholasIngolia
seqloc190.0Handle sequence locations for bioinformatics (bioinformatics, library, mit)2015-01-16NicholasIngolia
seqloc-datafiles280.0Read and write BED and GTF format genome annotations (bioinformatics, library, mit, program)2015-03-20NicholasIngolia
sequence-formats460.0A package with basic parsing utilities for several Bioinformatic data formats. (bioinformatics, gpl, library)2022-03-30stephan_schiffels
sequenceTools260.0A package with tools for processing DNA sequencing data (bioinformatics, gpl, library, program)2022-02-17stephan_schiffels
sgrep20.0Sgrep - grep Fasta files for sequences matching a regular expression (bioinformatics, program)2010-09-13KetilMalde
simseq10.0Simulate sequencing with different models for priming and errors (bioinformatics, program)2008-03-08GwernBranwen
slynx460.0Handle molecular sequences (bioinformatics, gpl, library, program)2022-02-22dschrempf
smiles110.0 (bioinformatics, bsd3, library)2017-08-15fonturacetamum
subsample40.0Subsample data. (bioinformatics, gpl, library, program)2018-05-16GregorySchwartz
tex-join-bib70.0Compile separate tex files with the same bibliography. (bioinformatics, gpl, library, program)2020-03-12GregorySchwartz
tlynx440.0Handle phylogenetic trees (bioinformatics, gpl, library, program)2022-02-22dschrempf
too-many-cells650.0Cluster single cells and analyze cell clade relationships. (bioinformatics, gpl, library, program)2021-03-03GregorySchwartz
trimpolya80.0Search for, annotate and trim poly-A tail (bioinformatics, program)2009-12-15KetilMalde
varan50.0Process mpileup output to identify significant differences (bioinformatics, program)2014-12-01KetilMalde
vcf12.0A package to parse VCF files inspired in similar python libraries (bioinformatics, library, mit)2017-08-10juanpaucar
xml2x30.0Convert BLAST output in XML format to CSV or HTML (bioinformatics, program)2009-10-07GwernBranwen, KetilMalde
xsact120.0Cluster EST sequences (bioinformatics, program)2010-09-09GwernBranwen, KetilMalde
zsyntax50.0Automated theorem prover for the Zsyntax biochemical calculus (bioinformatics, bsd3, library, logic, theorem-provers)2018-12-15fsestini