Search results for "distribution:BioPerl Bio::Align"
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
Bio::Align::Utilities - A collection of utilities regarding converting and manipulating alignment objects
This module contains utility methods for manipulating sequence alignments (Bio::Align::AlignI) objects. The aa_to_dna_aln utility is essentially the same as the mrtrans program by Bill Pearson available at ftp://ftp.virginia.edu/pub/fasta/other/mrtra...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Align::StatisticsI - Calculate some statistics for an alignment
Describe the interface here...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment
This object contains routines for calculating various statistics and distances for DNA alignments. The routines are not well tested and do contain errors at this point. Work is underway to correct them, but do not expect this code to give you the rig...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Align::ProteinStatistics - Calculate Protein Alignment statistics (mostly distances)
This object is for generating various statistics from a protein alignment. Mostly it is where pairwise protein distances can be calculated....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Align::PairwiseStatistics - Base statistic object for Pairwise Alignments
Calculate pairwise statistics....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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
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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::po - po MSA Sequence input/output stream
This object can transform 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', Bioi...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::maf - Multiple Alignment Format sequence input stream
This class constructs 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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::arp - ARP MSA Sequence input/output stream
This object can create 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 sequence...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::psi - Read/Write PSI-BLAST profile alignment files
This is a parser for psi-blast blocks....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::msf - msf sequence input/output stream
This object can transform Bio::Align::AlignI objects to and from msf flat file databases....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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)....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::xmfa - XMFA MSA Sequence input/output stream
This object can transform 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 parser wr...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::mase - mase sequence input/output stream
This object can transform Bio::Align::AlignI objects to and from mase flat file databases....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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 Bio::SimpleAlign objects. Each SimpleAlign object contains Bio::LocatableSeq objects which represent the individual aligned sites as ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::pfam - pfam sequence input/output stream
This object can transform Bio::SimpleAlign objects to and from pfam flat file databases....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::selex - selex sequence input/output stream
This object can transform Bio::Align::AlignI objects to and from selex flat file databases....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::nexus - NEXUS format sequence input/output stream
This object can transform Bio::Align::AlignI objects to and from NEXUS data blocks. See method documentation for supported NEXUS features....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC