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Alien-SeqAlignment-edlib-0.02
River stage zero No dependents
/ Alien::SeqAlignment::edlib

NAME

Alien::SeqAlignment::edlib

VERSION

version 0.02

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. It does this by first trying to detect an existing install of parasail on your system. If found it will use that. If it cannot be found, the source code will be downloaded from the internet and it will be installed in a private share location for the use of other modules. The build provides the static and shared libraries, but also the command line aligner (edlib-aligner, not currently available in Windows).

NAME

Alien::SeqAlignment::edlib - find, build and install the edlib library

METHODS

exe

 Alien::SeqAlignment::edlib->exe

Returns 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.

https://metacpan.org/pod/Text::Levenshtein::Edlib An XS library that also wraps around the edlib library and returns edit distances, as well as alignment paths.
https://metacpan.org/pod/Text::Levenshtein::XS An XS library that computes edit distances but not alignment paths. This module was updated last in 2016 (see also its github repository at: https://github.com/ugexe/Text--Levenshtein--XS/)
https://metacpan.org/pod/Text::LevenshteinXS Yet another XS implementation of Levenshtein distance over strings (no alignment path). This module was last updated in 2004.
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.