Search results for "Bio::AlignIO"
Bio::AlignIO - Handler for AlignIO Formats
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- Bio::AlignIO::po - po MSA Sequence input/output stream
- Bio::AlignIO::maf - Multiple Alignment Format sequence input stream
- Bio::AlignIO::arp - ARP MSA Sequence input/output stream
- 30 more results from BioPerl »
Bio::Index::Stockholm - Interface for indexing Stockholm files
Indexes Stockholm format alignments such as those from Pfam and Rfam. Returns raw stream data using the ID or a Bio::SimpleAlign object (via Bio::AlignIO). This module also allows for ID parsing using a callback: $inx->id_parser(\&get_id); # make the...
CJFIELDS/Bio-AlignIO-stockholm-1.7.3 - 25 Sep 2018 00:14:27 UTC - Search in distribution- Bio::AlignIO::stockholm - stockholm sequence input/output stream
FAST::Bio::AlignIO - Handler for AlignIO Formats
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- FAST::Bio::AlignIO::po - po MSA Sequence input/output stream
- FAST::Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
- FAST::Bio::AlignIO::arp - ARP MSA Sequence input/output stream
- 23 more results from FAST »
Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver
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::Gonzales::Align::IO - Utility functions for aligment stuff
JWB/Bio-Gonzales-0.083
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02 Jan 2021 23:10:48 UTC
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- Bio::Gonzales::Align::IO::Stockholm - IO class for the stockholm format
- lib/Bio/Gonzales/Align/IO/MAF.pm
- aln2aln - convert different alignment formats to another alignment format
Tutorial - Hands-on tutorial for using Bio::NEXUS module.
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
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...
YZHERNAND/Bio-BPWrapper-1.15 - 27 Feb 2024 16:55:31 UTC - Search in distribution- Bio::BPWrapper::AlnManipulations - Functions for bioaln
Bio::fastAPD - rapid calculation of average pairwise difference (APD) for multiple sequence alignments
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
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.
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
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::Tools::Run::Phylo::Phyml - Wrapper for rapid reconstruction of phylogenies using Phyml
- Bio::Factory::EMBOSS - EMBOSS application factory class
- Bio::Tools::Run::EMBOSSacd - class for EMBOSS Application qualifiers
- 18 more results from BioPerl-Run »
Bio::DB::HTS::Alignment - The HTS alignment object
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
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.
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
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
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
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
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- Bio::Tools::Run::Phylo::PAML::Baseml - Wrapper aroud the PAML program baseml
- Bio::Tools::Run::Phylo::PAML::Yn00 - Wrapper aroud the PAML program yn00