BioPerl - Perl Modules for Biology 11 ++

BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are advertised to do in the documen...

CJFIELDS/BioPerl-1.6.924 - 10 Jul 2014 20:22:23 GMT - Search in distribution

Bundle::BioPerl - A bundle to install external CPAN modules used by BioPerl 1.5.2 ++

The BioPerl distribution from http://bioperl.org contains code and modules that may use or require additional 'external' perl modules for advanced functionality. Many of the external modules are not contained within the standard Perl distribution. Th...

CJFIELDS/Bundle-BioPerl-2.1.9 - 16 Jan 2015 20:05:40 GMT - Search in distribution

Fry::Lib::BioPerl - Commandline enables common tasks for sequence and alignment objects for Bio::Perl modules. ++

The main point of this library is to view,retrieve and create sequences and alignments. All objects created are indexed by the shell as Fry::Obj objects. See Fry::Lib::Default for commands that you can perform on these objects. Sequence and alignment...

BOZO/Fry-Lib-BioPerl-0.15 - 14 Jan 2005 20:54:17 GMT - Search in distribution

Dist::Zilla::PluginBundle::Bioperl - Build your distributions like Bioperl does ++

This is the Dist::Zilla configuration I use to build my distributions. It is roughly equivalent to: [@Filter] bundle = @Basic [MetaConfig] [MetaJSON] [PkgVersion] [PodSyntaxTests] [PodCoverageTests] [NoTabsTests] [EOLTests] [NextRelease] [Git::Tag] [...

RBUELS/Dist-Zilla-PluginBundle-Bioperl-0.01 - 13 Oct 2011 20:57:52 GMT - Search in distribution

Pod::Weaver::PluginBundle::BioPerl - Configure your POD like Bioperl does 3 ++

This is the Pod::Weaver configuration for the BioPerl project. It is roughly equivalent to: [@CorePrep] [Name] [Version] [Region / prelude] [Generic / SYNOPSIS] [Generic / DESCRIPTION] [Generic / OVERVIEW] [Collect / ATTRIBUTES] command = attr [Colle...

CJFIELDS/Dist-Zilla-PluginBundle-BioPerl-0.23 - 05 Sep 2014 14:47:10 GMT - Search in distribution


Bio::DB::DBD - DESCRIPTION of Interface ++

of Interface SYNOPSIS Give standard usage here DESCRIPTION Describe the interface here FEEDBACK Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the B...

CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 GMT - Search in distribution

Bio::DB::ESoap - Client for the NCBI Entrez EUtilities SOAP server ++

"ESoap" provides a basic SOAP interface to the NCBI Entrez Utilities Web Service (<http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/DOC/esoap_help.ht ml>). SOAP::Lite handles the SOAP calls. Higher level access, pipelines, BioPerl object I/O an...

CJFIELDS/BioPerl-Run-1.006900 - 21 Apr 2011 16:23:41 GMT - Search in distribution

Bio::Network::IO - Class for reading and writing biological network data. ++

This class is analagous to the SeqIO and AlignIO classes. To read in a file of a particular format, file and format are given as key/value pairs as arguments. The Bio::Network::IO checks that the appropriate module is available and loads it. At prese...

CJFIELDS/BioPerl-Network-1.006902 - 07 Nov 2011 16:27:40 GMT - Search in distribution

Bio::ORA - Olfactory Receptor family Assigner (bioperl module) ++

Bio::ORA is a featherweight object for identifying mammalian olfactory receptor genes. The sequences should not be longer than 20kb. The returned array include location, sequence and statistic for the putative olfactory receptor gene. Fully functiona...

CERATITES/ora-1.9 - 22 Apr 2013 15:00:12 GMT - Search in distribution

Bio::mGen - a fast and simple gene loading, helping automate BioPerl processes. ++

"Bio::mGen" This module extracts pre-parsed compressed DNA from "Genbank" and "Refseq" (soon more) databases without draining the NCBI web server resources. Guaranteed to work faster than any module because of the features: Parse-free, compression en...

CYBER/mGen-1.03 - 14 Jan 2006 10:04:36 GMT - Search in distribution

FAST::Bio::UnivAln - Bioperl alignment object ++

This module is the FAST::Bio::UnivAln alignment object which is part of the Bioperl project. Currently it has some nice methods for accessing an alignment after reading it in from certain formats, incl. utilities like consensus and reverse complement...

DHARD/FAST-1.03 - 12 Feb 2015 19:02:27 GMT - Search in distribution

bp_biblio - bioperl client for accessing and querying a bibliographic repository 3 ++

A client showing how to use Bio::Biblio module, a module for accessing and querying a bibliographic repository. It also shows how to use modules Bio::Biblio::IO::medlinexml Bio::Biblio::IO::medline2ref which converts XML MEDLINE citations into a simp...

CDRAUG/Bio-Biblio-1.70 - 24 Mar 2013 00:19:52 GMT - Search in distribution

Mecom - A Perl module for protein contact interfaces evolutive analysis ++

This module integrates a workflow aimed to address the evolvability of the contact interfaces within a protein complex. The method "Mecom->run" launchs the whole analysis. Also, such workflow is divided into the following steps: Step 1, Structural an...

HVALVERDE/Mecom-1.15 - 13 Jul 2013 18:55:01 GMT - Search in distribution
  • Mecom - A Perl program for protein contact interfaces evolutive analysis

align2nex.pl - translate an alignment into NEXUS format using BioPerl ++

Output the alignment in <infile> in NEXUS format. This is dependent on BioPerl AlignIO modules. I don't know how well it will work. OPTIONS -f, --format The format of the input file. One of { bl2seq, clustalw, emboss, fasta, mase, mega, meme, msf, ne...

ARLIN/Bio-NEXUS-0.78   (1 review) - 10 Feb 2012 13:31:13 GMT - Search in distribution

BioUtil - Bioinformatics Utilities! 2 ++
SHENWEI/BioUtil-2015.03092 - 09 Mar 2015 13:06:06 GMT - Search in distribution

SeqDiff - A tool to find the differences between two Seq objects. ++

The SeqDiff tool presented here will compare two Bio::Seq objects. It first looks through both objects and matches their features based on some criteria. It then recursively compares each pair of features and returns the comparison. Originally the pa...

BLUECURIO/SeqDiff-v0.1 - 12 Feb 2010 16:18:40 GMT - Search in distribution

GD::SVG - Seamlessly enable SVG output from scripts written using GD 1 ++

GD::SVG painlessly enables scripts that utilize GD to export scalable vector graphics (SVG). It accomplishes this task by wrapping SVG.pm with GD-styled method calls. To enable this functionality, one need only change the "use GD" call to "use GD::SV...

TWH/GD-SVG-0.33 - 10 May 2009 14:39:31 GMT - Search in distribution

HackaMol - HackaMol: Object-Oriented Library for Molecular Hacking ++

The HackaMol library simplifies powerful scripting of multiscale molecular modeling and analysis. HackaMol seeks to provide intuitive attributes and methods that may be harnessed to coerce molecular computation through a common core. The library is i...

DEMIAN/HackaMol-0.017 - 27 Feb 2015 14:16:31 GMT - Search in distribution

AlignAid - easily run sequence alignments locally or on a cluster ++

AlignAid is designed to make it easy to run the sequence alignment programs Blast and cross_match. AlignAid can accept a large number of query sequences. If a compute cluster queue such as LSF or PBS is available, AlignAid can automatically split the...

DMESSINA/AlignAid-v0.0.2 - 16 Dec 2006 01:04:35 GMT - Search in distribution