Search results for "Bio::Align"
Bio::Align::Subset - A BioPerl module to generate new alignments as subset from larger alignments
Given an array of codon positions and an alignment, the function Bio::Align::Subset->build_subset returns a new alignment with the codons at those positions from the original alignment....
HVALVERDE/Bio-Align-Subset-1.27 - 08 May 2013 17:33:42 UTC - Search in distribution
Bio::Align::AlignI - An interface for describing sequence alignments.
This interface describes the basis for alignment objects....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects
- Bio::Align::StatisticsI - Calculate some statistics for an alignment
- Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment
- 30 more results from BioPerl »
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::Prospect::Align - Package for overlaying multiple Prospect alignments
Bio::Prospect::Align represents an alignment of one or more Prospect structural alignments....
REECE/Bio-Prospect-1.04 - 19 Nov 2003 06:34:27 UTC - Search in distribution- Bio::Prospect::Thread - Representation of a Prospect thread.
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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FAST::Bio::Align::AlignI - An interface for describing sequence alignments.
This interface describes the basis for alignment objects....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::AlignIO - Handler for AlignIO Formats
- FAST::Bio::SimpleAlign - Multiple alignments held as a set of sequences
- FAST::Bio::AlignIO::po - po MSA Sequence input/output stream
- 26 more results from FAST »
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
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::DB::HTS::AlignWrapper - Add high-level methods to Bio::DB::HTS::Alignment
This is a wrapper around Bio::DB::HTS::Alignment that adds the following high-level methods. These are described in detail in "High-level Bio::DB::HTS::Alignment methods" in Bio::DB::HTS::Alignment. add_segment() add a new subfeature to split alignme...
AVULLO/Bio-DB-HTS-3.01 - 23 Apr 2019 13:51:11 UTC - Search in distribution- Bio::DB::HTS - Read files using HTSlib including BAM/CRAM, Tabix and BCF database files
- Bio::DB::HTS::Query - Object representing the query portion of a BAM/SAM alignment
- Bio::DB::HTS::Alignment - The HTS alignment object
Bio::DB::Bam::AlignWrapper - Add high-level methods to Bio::DB::Bam::Alignment
This is a wrapper around Bio::DB::Bam::Alignment that adds the following high-level methods. These are described in detail in "High-level Bio::DB::Bam::Alignment methods" in Bio::DB::Bam::Alignment. add_segment() add a new subfeature to split alignme...
LDS/Bio-SamTools-1.43 - 12 Feb 2016 19:33:32 UTC - Search in distribution- Bio::DB::Sam - Read SAM/BAM database files
- Bio::DB::Bam::Query - Object representing the query portion of a BAM/SAM alignment
- Bio::DB::Bam::Alignment - The SAM/BAM alignment object
Bio::Graphics::Browser::CAlign - Compiled helper for Bio::Graphics::Browser::Realign
This module is used internally by Bio::Graphics::Browser::Realign. If the module is present, the Smith-Waterman alignment will be faster. Otherwise, Bio::Graphics::Browser::Realign will fall back to a slower pure-perl implementation....
LDS/GBrowse-2.56 - 15 Jan 2017 21:29:11 UTC - Search in distribution- Bio::Graphics::Browser2::CAlign - Compiled helper for Bio::Graphics::Browser::Realign
- Bio::Graphics::Browser2::Plugin::AlignTwoSequences - a plugin that executes NCBI's bl2seq on the current view
- pod::CONFIGURE_HOWTO
- 2 more results from GBrowse »
Bio::Graphics::Glyph::phylo_align - The "phylogenetic alignment" glyph
This glyph draws a cladogram for any set of species along with their alignment data in relation to the reference species. At high magnification, base pair alignements will be displayed. At lower magnification, a conservation score plot will be drawn....
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC - Search in distribution- Bio::Graphics::Glyph::trace - A glyph that visualizes a trace file
- Bio::Graphics::Glyph::segments - The "segments" glyph
Bio::MUST::Apps::TwoScalp::AlignAll - internal class for two-scalp tool
# TODO...
DBAURAIN/Bio-MUST-Apps-TwoScalp-0.231010 - 11 Apr 2023 09:35:17 UTC - Search in distribution- Bio::MUST::Apps::TwoScalp - Main class for two-scalp tool
lib/Bio/Emboss/Methods.pm
PERNST/Bio-Emboss-5.0.0.1
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06 Sep 2007 16:28:46 UTC
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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....
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
FortyTwo::Manual - User Guide for Forty-Two
DBAURAIN/Bio-MUST-Apps-FortyTwo-0.213470
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13 Dec 2021 23:13:33 UTC
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- Bio::MUST::Apps::FortyTwo - Main class for forty-two tool
Bio::Grep - Perl extension for searching in DNA and Protein sequences
Bio-Grep is a collection of Perl modules for searching in DNA and Protein sequences. It supports different back-ends, most importantly some (enhanced) suffix array implementations. Currently, there is no suffix array tool that works in all scenarios ...
LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC - Search in distribution
bp_pairwise_kaks - calculate pairwise Ka,Ks for a set of sequences
This script will take as input a dataset of cDNA sequences, verify that they contain no stop codons, align them in protein space, project the alignment back into cDNA, and estimate the Ka (non-synonymous) and Ks (synonymous) substitutions based on th...
CDRAUG/Bio-Tools-Phylo-PAML-1.7.3 - 01 Jul 2018 12:36:38 UTC - Search in distribution- Bio::Tools::Run::Phylo::PAML::Codeml - Wrapper aroud the PAML program codeml
- Bio::Tools::Run::Phylo::PAML::Baseml - Wrapper aroud the PAML program baseml
- Bio::Tools::Run::Phylo::PAML::Yn00 - Wrapper aroud the PAML program yn00
- 1 more result from Bio-Tools-Phylo-PAML »