Bio::Tools::Phylo::PAML - Parses output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00 River stage one • 1 direct dependent • 1 total dependent

This module is used to parse the output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio::Tools::Run::Phylo::PAML::* modules to actually run some of the PAML programs, but this module is only useful to parse t...

CDRAUG/Bio-Tools-Phylo-PAML-1.7.3 - 01 Jul 2018 12:36:38 UTC - Search in distribution

Bio::LITE::Taxonomy::RDP - Lightweight and efficient RDP taxonomic manager River stage zero No dependents

This module provides easy and efficient access to the RDP taxonomy with minimal dependencies and without intermediary databases. This module is not part of the Bioperl bundle....

MOTIF/Bio-LITE-Taxonomy-RDP-0.03 - 24 May 2011 11:21:02 UTC - Search in distribution

Bio::Sampling::Valection River stage zero No dependents

Bio::Sampling::Valection - Sampler for verification Bio::Sampling::Valection contains a variety of algorithms for choosing verification candidates from competing tools or parameterizations, to fairly assess their performance against each other. Origi...

BOUTROSLB/Bio-Sampling-Valection-v1.0.1 - 23 Nov 2017 20:49:55 UTC - Search in distribution

Bio::Tools::Primer3Redux River stage zero No dependents

Bio::Tools::Primer3Redux creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3 output files. This module provides a bioperl interface to the program primer3. See http://www-genome.wi.mit....

CJFIELDS/Bio-Tools-Primer3Redux-0.09 - 11 Jun 2011 04:03:42 UTC - Search in distribution

Bio::DB::Taxonomy::sqlite - SQLite-based implementation of Bio::DB::Taxonomy::flatfile River stage zero No dependents

This is an implementation of Bio::DB::Taxonomy which stores and accesses the NCBI taxonomy using a simple SQLite3 database stored locally on disk. With this implementation, one can do the same basic searches as with the 'flatfile' database. A test lo...

CJFIELDS/Bio-DB-Taxonomy-sqlite-1.7.3 - 02 Mar 2020 05:53:54 UTC - Search in distribution

Bio::LITE::Taxonomy::NCBI - Lightweight and efficient NCBI taxonomic manager River stage one • 1 direct dependent • 8 total dependents

This module provides easy and efficient access to the NCBI taxonomy with minimal dependencies and without intermediary databases. This module is not part of the Bioperl bundle. For bioperl alternatives see the "SEE ALSO" section of this document....

MOTIF/Bio-LITE-Taxonomy-NCBI-0.1 - 20 May 2015 08:51:23 UTC - Search in distribution

Bio::MUST::Apps::Physeter - Dummy internal class for physeter tool River stage zero No dependents

DBAURAIN/Bio-MUST-Apps-Physeter-0.202960 - 22 Oct 2020 14:00:58 UTC - Search in distribution

Bio::MUST::Apps::TwoScalp - Main class for two-scalp tool River stage zero No dependents

"two-scapl.pl" is an application to align or re-align sequences in existing multiple sequences alignments (FASTA or ALI file formats). Its main engine is BLAST <https://blast.ncbi.nlm.nih.gov/>. Note that only alignable regions of the sequences are a...

DBAURAIN/Bio-MUST-Apps-TwoScalp-0.201810 - 29 Jun 2020 13:24:05 UTC - Search in distribution

Bio::PDB::Structure::Atom - Perl module for parsing and manipulating Protein Databank (PDB) files River stage zero No dependents

This module combines tools that are commonly used to analyze proteins and nucleic acids from a pdb file stuctures. The main benefits of using the module are its ability to parse and print out a pdb structure with minimum effort. However in addition t...

RULIX/Bio-PDB-Structure-0.02 - 22 Jul 2012 15:49:40 UTC - Search in distribution

Bio::SAGE::DataProcessing - Processes raw serial analysis of gene expression (SAGE) data. River stage zero No dependents

This module provides several tools for processing and analyzing serial analysis of gene expression (SAGE) libraries....

SCOTTZED/Bio-SAGE-DataProcessing-1.20 - 15 Oct 2004 22:37:38 UTC - Search in distribution

Bio::Tools::CodonOptTable - A more elaborative way to check the codons usage! River stage zero No dependents

The purpose of this module is to show codon usage. We produces each codon frequency, Relative Synonymous Codons Uses and Relative Adaptiveness of a Codon table and bar graph that will help you to calculate the Codon Adaptation Index (CAI) of a gene, ...

SHARDIWAL/Bio-Tools-CodonOptTable-1.05 - 16 Sep 2010 01:15:35 UTC - Search in distribution


Bio::App::SELEX::Stockholm River stage zero No dependents

MOLECULES/Bio-App-SELEX-RNAmotifAnalysis-0.0095 - 10 Apr 2014 14:22:57 UTC - Search in distribution

Bio::GMOD::GenericGenePage - Generic GMOD gene page base class River stage zero No dependents

Bio::GMOD::GenericGenePage is an abstract class to make it easier for Model Organism Databases (MODs) to serve up a simple XML that describes attributes of their gene models. In order to implement this, the user needs to subclass Bio::GMOD::GenericGe...

SCAIN/Bio-GMOD-GenericGenePage-0.12 - 24 Mar 2010 19:38:26 UTC - Search in distribution

Bio::Phylo::Forest::DBTree - Phylogenetic database as a tree object River stage zero No dependents

This package provides the functionality to handle very large phylogenies (examples: the NCBI taxonomy, the Green Genes tree) as if they are Bio::Phylo tree objects, with all the possibilities for traversal, computation, serialization, and visualizati...

RVOSA/Bio-Phylo-Forest-DBTree-v0.1.2 - 24 Oct 2017 14:06:26 UTC - Search in distribution

Bio::Taxonomy::GlobalNames - Perlish OO bindings to the Global Names Resolver API River stage zero No dependents

Bio::Taxonomy::GlobalNames provides Perl objects and functions that interface with the Global Names Resolver web service. Using a REST client, input is sent to the service, whereas results are internally converted from JSON format to nested objects a...

DGKONTOP/Bio-Taxonomy-GlobalNames-0.07 - 22 Dec 2014 22:34:39 UTC - Search in distribution

Bio::Tree::Draw::Cladogram - Drawing phylogenetic trees in Encapsulated PostScript (EPS) format. River stage zero No dependents

Bio::Tree::Draw::Cladogram is a Perl tool for drawing Bio::Tree::Tree objects in Encapsulated PostScript (EPS) format. It can be utilized both for displaying a single phylogenetic tree (a cladogram) and for the comparative display of two phylogenetic...

CJFIELDS/Bio-Tree-Draw-Cladogram-1.7.3 - 25 Sep 2018 01:26:07 UTC - Search in distribution

Catalyst::View::Bio::SeqIO - use BioPerl's Bio::SeqIO as a Catalyst view River stage one • 1 direct dependent • 1 total dependent

RBUELS/Catalyst-View-Bio-SeqIO-0.02 - 21 Feb 2011 06:44:36 UTC - Search in distribution

Webservice::InterMine::Bio - Access data from InterMine queries in biological formats. River stage zero No dependents

INTERMINE/Webservice-InterMine-Bio-0.9900 - 10 Jan 2012 19:14:07 UTC - Search in distribution

Bio::JBrowse::FeatureStream River stage zero No dependents

RBUELS/Bio-JBrowse-Store-NCList-0.1 - 06 Aug 2013 19:07:18 UTC - Search in distribution

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