Bio::AlignIO - Handler for AlignIO Formats River stage two • 60 direct dependents • 65 total dependents

Bio::AlignIO is a handler module for the formats in the AlignIO set, for example, Bio::AlignIO::fasta. It is the officially sanctioned way of getting at the alignment objects. The resulting alignment is a Bio::Align::AlignI-compliant object. The idea...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution

FAST::Bio::AlignIO - Handler for AlignIO Formats River stage zero No dependents

FAST::Bio::AlignIO is a handler module for the formats in the AlignIO set, for example, FAST::Bio::AlignIO::fasta. It is the officially sanctioned way of getting at the alignment objects. The resulting alignment is a FAST::Bio::Align::AlignI-complian...

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

Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver River stage zero No dependents

This object can transform Bio::SimpleAlign objects to and from NeXML format. For more information on NeXML, visit <http://www.nexml.org>....

CJFIELDS/Bio-NeXMLIO-1.7.3 - 11 Sep 2018 18:47:25 UTC - Search in distribution
  • Bio::NexmlIO - stream handler for NeXML documents
  • Bio::Nexml::Factory - A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents

Bio::AlignIO::stockholm - stockholm sequence input/output stream River stage one • 1 direct dependent • 1 total dependent

This object can transform Bio::Align::AlignI objects to and from stockholm flat file databases. This has been completely refactored from the original stockholm parser to handle annotation data and now includes a write_aln() method for (almost) comple...

CJFIELDS/Bio-AlignIO-stockholm-1.7.3 - 25 Sep 2018 00:14:27 UTC - Search in distribution

Bio::Gonzales::Align::IO - Utility functions for aligment stuff River stage zero No dependents

JWB/Bio-Gonzales-0.083 - 02 Jan 2021 23:10:48 UTC - Search in distribution

Tutorial - Hands-on tutorial for using Bio::NEXUS module. River stage one • 1 direct dependent • 1 total dependent

Tutorial to get started using Bio::NEXUS module. INTRODUCTION The NEXUS file format standard of Maddison, et al. (1997) is designed to represent sets of data, including character data (e.g., molecular sequence alignments, morphological character sets...

ARLIN/Bio-NEXUS-0.78 - 10 Feb 2012 13:31:13 UTC - Search in distribution

bioaln - Alignment manipulations based on BioPerl River stage zero No dependents

bioaln performs common, routine manipulations of sequence alignments based on BioPerl modules including Bio::AlignIO, Bio::SimpleAlign and Bio::Align::Utilities. By default, bioaln assumes that both the input and the output files are in CLUSTALW form...

ROCKY/Bio-BPWrapper-1.13 - 02 Apr 2020 19:04:03 UTC - Search in distribution

Bio::fastAPD - rapid calculation of average pairwise difference (APD) for multiple sequence alignments River stage zero No dependents

The Bio::fastAPD module provides a computationally efficient method for the calculation of average pairwise difference (APD), a measure of nucleotide diversity, from multiple sequence alignment (MSA) data. This module also provides rapid standard err...

JDBAUGHER/Bio-fastAPD-1.10.0 - 08 Apr 2015 20:59:21 UTC - Search in distribution

Bio::EasyYang - A tiny interface for Bio::Tools::Run::Phylo::PAML::Yn00 module River stage zero No dependents

This module is a simple function to execute the Yang algorithm easily....

HVALVERDE/Bio-EasyYang-1 - 13 Nov 2012 10:46:20 UTC - Search in distribution

Bio::Network::IO - Class for reading and writing biological network data. River stage zero No dependents

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 UTC - Search in distribution

Bio::Tools::Run::Vista - Wrapper for Vista River stage one • 2 direct dependents • 2 total dependents

Pls see Vista documentation for plotfile options Wrapper for Vista : C. Mayor, M. Brudno, J. R. Schwartz, A. Poliakov, E. M. Rubin, K. A. Frazer, L. S. Pachter, I. Dubchak. VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinf...

CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution

Bio::DB::HTS::Alignment - The HTS alignment object River stage one • 1 direct dependent • 1 total dependent

The Bio::DB::HTS::Alignment and Bio::DB::HTS::AlignWrapper classes together represent an alignment between a sequence read (the "query") and a reference sequence (the "target"). Bio::DB::HTS::Alignment adheres strictly to the C-level BAM library's de...

AVULLO/Bio-DB-HTS-3.01 - 23 Apr 2019 13:51:11 UTC - Search in distribution

Bio::DB::Bam::Alignment - The SAM/BAM alignment object River stage one • 1 direct dependent • 1 total dependent

The Bio::DB::Bam::Alignment and Bio::DB::Bam::AlignWrapper classes together represent an alignment between a sequence read (the "query") and a reference sequence (the "target"). Bio::DB::Bam::Alignment adheres strictly to the C-level BAM library's de...

LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC - Search in distribution

Fry::Lib::BioPerl - Commandline enables common tasks for sequence and alignment objects for Bio::Perl modules. River stage zero No dependents

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 UTC - Search in distribution

Bio::Grep::SearchResult - Data structure for a back-end search hit River stage zero No dependents

Bio::Grep::SearchResult is the data structure for one hit in the database....

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC - Search in distribution

Bio::Align::Graphics - Graphic Rendering of Bio::Align::AlignI Objects River stage one • 1 direct dependent • 1 total dependent

Bio::Align::Graphics is a module designed to create image files out of Bio::Align::AlignI objects. An alignment may be manipulated with various formatting and highlighting options. An example: #!/usr/bin/perl -w use Bio::AlignIO; use Bio::Align::Grap...

CJFIELDS/Bio-Align-Graphics-1.7.3 - 25 Sep 2018 00:17:21 UTC - Search in distribution

Bio::Tools::Run::Alignment::Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program River stage zero No dependents

Note: this DESCRIPTION only documents the Bioperl interface to Clustalw. Clustalw, itself, is a large & complex program - for more information regarding clustalw, please see the clustalw documentation which accompanies the clustalw distribution. Clus...

CDRAUG/Bio-Tools-Run-Alignment-Clustalw-1.7.4 - 11 Jul 2018 14:57:04 UTC - Search in distribution

Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml River stage one • 1 direct dependent • 1 total dependent

This is a wrapper around the codeml program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information. This module is more about generating the properl codem...

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