Search results for "dist:FAST Bio::Align"
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
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
FAST::Bio::SimpleAlign - Multiple alignments held as a set of sequences
SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipula...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::po - po MSA Sequence input/output stream
This object can transform FAST::Bio::SimpleAlign objects to and from 'po' format flat file databases. 'po' format is the native format of the POA alignment program (Lee C, Grasso C, Sharlow MF, 'Multiple sequence alignment using partial order graphs'...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
This is a parser for psi-blast blocks....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::arp - ARP MSA Sequence input/output stream
This object can create FAST::Bio::SimpleAlign objects from ARP flat files. These are typically configuration-like data files for the program Arlequin. For more information, see: http://lgb.unige.ch/arlequin/ For the moment, this retains the allele se...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::msf - msf sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from msf flat file databases....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::maf - Multiple Alignment Format sequence input stream
This class constructs FAST::Bio::SimpleAlign objects from an MAF-format multiple alignment file. Writing in MAF format is currently unimplemented. Spec of MAF format is here: http://genome.ucsc.edu/FAQ/FAQformat...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::pfam - pfam sequence input/output stream
This object can transform FAST::Bio::SimpleAlign objects to and from pfam flat file databases....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream
This object can transform FAST::Bio::SimpleAlign objects from XMFA flat file databases. For more information, see: http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html This module is based on the AlignIO::fasta par...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::meme - meme sequence input/output stream
This object transforms the "sites sorted by position p-value" sections of a meme (text) output file into a series of FAST::Bio::SimpleAlign objects. Each SimpleAlign object contains FAST::Bio::LocatableSeq objects which represent the individual align...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::mase - mase sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from mase flat file databases....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::mega - Parse and Create MEGA format data files
This object handles reading and writing data streams in the MEGA format (Kumar and Nei)....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::nexml - NeXML format sequence alignment input/output stream driver
This object can transform FAST::Bio::SimpleAlign objects to and from NeXML format. For more information on NeXML, visit <http://www.nexml.org>....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::selex - selex sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from selex flat file databases....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
This object can transform FAST::Bio::SimpleAlign objects to and from fasta flat file databases. This is for the fasta alignment format, not for the FastA sequence analysis program. To process the alignments from FastA (FastX, FastN, FastP, tFastA, et...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::proda - proda sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from proda files....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::nexus - NEXUS format sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from NEXUS data blocks. See method documentation for supported NEXUS features....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::prodom - prodom sequence input/output stream
This object can transform FAST::Bio::Align::AlignI objects to and from prodom flat file databases....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC
FAST::Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)
This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC