Search results for "Bio::Symbol::Alphabet"
perlop - Perl operators and precedence
In Perl, the operator determines what operation is performed, independent of the type of the operands. For example "$x + $y" is always a numeric addition, and if $x or $y do not contain numbers, an attempt is made to convert them to numbers first. Th...
RJBS/perl-5.36.0 - 28 May 2022 00:26:10 UTC - Search in distribution- perlop - Perl operators and precedence
FAST::Bio::UnivAln - Bioperl alignment object
This module is the FAST::Bio::UnivAln alignment object which is part of the Bioperl project. Currently it has some nice methods for accessing an alignment after reading it in from certain formats, incl. utilities like consensus and reverse complement...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::SimpleAlign - Multiple alignments held as a set of sequences
- FAST::Bio::SeqIO::chadoxml - chadoxml sequence output stream
- FAST::Bio::Tools::SeqPattern - represent a sequence pattern or motif
- 2 more results from 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...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::Matrix::PSM::SiteMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds
- Bio::Tools::IUPAC - Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence
- Bio::Align::DNAStatistics - Calculate some statistics for a DNA alignment
- 2 more results from BioPerl »
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::Variation::SeqDiff - Container class for mutation/variant descriptions
SeqDiff stores Bio::Variation::VariantI object references and descriptive information common to all changes in a sequence. Mutations are understood to be any kind of sequence markers and are expected to occur in the same chromosome. See Bio::Variatio...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC - Search in distribution
Bio::AlignIO::stockholm - stockholm sequence input/output stream
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::Phylo::Matrices::Datatype - Validator of character state data
This is a superclass for objects that validate character data. Objects that inherit from this class (typically those in the Bio::Phylo::Matrices::Datatype::* namespace) can check strings and arrays of character data for invalid symbols, and split and...
RVOSA/Bio-Phylo-v2.0.1 - 30 Oct 2017 19:50:35 UTC - Search in distribution