BioPerl - Perl Modules for Biology

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-1.007001 - 06 Nov 2016 04:02:23 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 for the BioPerl project. It is roughly equivalent to: [@Filter] -bundle = @Basic ; the basic to maintain and release CPAN distros -remove = Readme ; avoid conflict since we already have a README file [MetaConfig]...

CDRAUG/Dist-Zilla-PluginBundle-BioPerl-0.25 - 18 Feb 2017 19:08:07 GMT - Search in distribution

lib/Bio/Gonzales/Role/BioPerl/Constructor.pm

JWB/Bio-Gonzales-0.062 - 16 Sep 2016 06:22:12 GMT - Search in distribution

Bio::DB::DBI - DESCRIPTION of Interface

Describe the interface here...

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. html>). SOAP::Lite handles the SOAP calls. Higher level access, pipelines, BioPerl object I/O an...

CJFIELDS/BioPerl-Run-1.007001 - 19 Dec 2016 04:28:18 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 (ORA) [bioperl module]

Bio::ORA is a featherweight object for identifying mammalian olfactory receptor genes. The sequences should not be longer than 40kb. The returned array include location, sequence and statistic for the putative olfactory receptor gene. Fully functiona...

CERATITES/ora-2.0 - 14 Jun 2016 15:58:05 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

bioseq - FASTA sequence utility based on Bio::Perl

ROCKY/Bio-BPWrapper-1.11 - 02 Jul 2016 04:08:09 GMT - Search in distribution

Mecom - A Perl program for protein contact interfaces evolutive analysis

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

fasxl - translate sequences by a genetic code.

fasxl takes multifasta format DNA or RNA codon sequences or alignments as input, and generates biological translations of those sequences as output. Gapped sequences on input are allowed with the -g, -k or -o options; the gap character "-" is require...

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 GMT - Search in distribution

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

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

RFC

JUGUANG/AutoSQL-0.2 - 25 Mar 2004 12:08:08 GMT - Search in distribution

Bio::Trace::ABIF - Perl extension for reading and parsing ABIF (Applied Biosystems, Inc. Format) files

VITA/Bio-Trace-ABIF-1.06 - 02 Nov 2016 11:16:32 GMT - Search in distribution

Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files

This module provides a Perl interface to the HTSlib library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across...

RISHIDEV/Bio-DB-HTS-2.7 - 03 Jan 2017 13:23:46 GMT - Search in distribution

Module::Build::API - API Reference for Module Authors

I list here some of the most important methods in "Module::Build". Normally you won't need to deal with these methods unless you want to subclass "Module::Build". But since one of the reasons I created this module in the first place was so that subcl...

LEONT/Module-Build-0.4222 - 30 Mar 2017 14:17:25 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

Bio::Graphics::Panel - Generate GD images of Bio::Seq objects

The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature and Das::Segment::Feature objects. It can be used to draw sequence annotations, ph...

CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 GMT - Search in distribution

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