NAME
Alien::SeqAlignment::edlib
VERSION
version 0.03
SYNOPSIS
To execute the alignment using the commande line tool:
use Alien::Edlib;
use Env qw( @PATH );
unshift @PATH, Alien::SeqAlignment::edlib->bin_dir;
system Alien::SeqAlignment::edlib->exe, (list of options), <queries.fasta>, <target.fasta>;DESCRIPTION
This distribution provides edlib so that it can be used by other Perl distributions that are on CPAN. The source code will be downloaded from the edlib github repo, and if that fails it will use the location of a fork but the author of this module. Contrary to other Alien modules, this one will not test for a prior install of the edlib library, but will install from source into a private share location for the use by other modules. This strategy will avoid overwritting prior system installs of the edlib library, and is guaranteed to use the latest version of edlib. The build provides the static and shared libraries, but also the CLI aligner (edlib-aligner, not currently available in Windows).
NAME
Alien::SeqAlignment::edlib - find, build and install the edlib library
METHODS
exe
Alien::SeqAlignment::edlib->exeReturns the command name for running the CLI version of the edlib aligner Since the command line tool is not built under Windows by the edlib project make files, this method will return undef under Windows.
HELPERS
%{edlib_aligner}
edlib_aligner
Returns the CLI command for the edlib aligner
SEE ALSO
- edlib
-
Edlib is a lightweight and superfast C/C++ library for sequence alignment using the edit (Levenshtein) distance between two or more biological (usually) sequences. It can calculate the edit distance, find the optimal aligment path and the coordinates (start/end) locations. It supports multiple alignment modes such as global (NW), prefix (SHW) and infix (HW). The library does not handle utf8 and its primary use is to compute edit distances and alignments over small (255 characters or fewer) alphabets as they occur in bioinformatic applications.
- Text::Levenshtein::Edlib
-
An XS library that also wraps around the edlib library and returns edit distances, as well as alignment paths.
- Text::Levenshtein::XS
-
An XS library that computes edit distances but not alignment paths. See also its github repository at: https://github.com/ugexe/Text--Levenshtein--XS/)
- Text::LevenshteinXS
-
Yet another XS implementation of Levenshtein distance over strings (no alignment path).
- Alien
-
Documentation on the Alien concept itself.
- Alien::Base
-
The base class for this Alien.
- Alien::Build::Manual::AlienUser
-
Detailed manual for users of Alien classes.
AUTHOR
Christos Argyropoulos <chrisarg@gmail.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2023 by Christos Argyropoulos.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.
AUTHOR
Christos Argyropoulos <chrisarg@gmail.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2023 by Christos Argyropoulos.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.