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
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 - 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 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
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
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
DBAURAIN/Bio-MUST-Apps-Physeter-0.202960 - 22 Oct 2020 14:00:58 UTC - Search in distribution
"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
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
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::SAGE::DataProcessing::Filter - An abstract filter for determining whether a [di]tag is worth keeping.
- Bio::SAGE::DataProcessing::MinimumPhredFilter - A filter that validates sequences based on minimum Phred score.
- Bio::SAGE::DataProcessing::AveragePhredFilter - A filter that validates sequences based on average Phred score.
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
RVOSA/Bio-PhyloXS-v0.1.0 - 13 Oct 2017 10:29:06 UTC - Search in distribution
MOLECULES/Bio-App-SELEX-RNAmotifAnalysis-0.0095 - 10 Apr 2014 14:22:57 UTC - Search in distribution
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
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 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 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
RBUELS/Catalyst-View-Bio-SeqIO-0.02 - 21 Feb 2011 06:44:36 UTC - Search in distribution
INTERMINE/Webservice-InterMine-Bio-0.9900 - 10 Jan 2012 19:14:07 UTC - Search in distribution
RBUELS/Bio-JBrowse-Store-NCList-0.1 - 06 Aug 2013 19:07:18 UTC - Search in distribution