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#!/usr/bin/env perl
# PODNAME: phylip2ali.pl
# ABSTRACT: Convert PHYLIP files to ALI files

use Modern::Perl '2011';
use autodie;

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdMapper';


for my $infile (@ARGV_infiles) {

    ### Processing: $infile
    my $ali = Ali->load_phylip($infile);

    if ($ARGV_map_ids) {
        my $idmfile = change_suffix($infile, '.idm');
        my $idm = IdMapper->load($idmfile);
        ### Restoring seq ids from: $idmfile
        $ali->restore_ids($idm);
    }

    my $outfile = change_suffix($infile, '.ali');
    $ali->store($outfile);
}

__END__

=pod

=head1 NAME

phylip2ali.pl - Convert PHYLIP files to ALI files

=head1 VERSION

version 0.252040

=head1 USAGE

    phylip2ali.pl <infiles> [optional arguments]

=head1 REQUIRED ARGUMENTS

=over

=item <infiles>

Path to input PHYLIP files [repeatable argument].

=for Euclid: infiles.type: readable
    repeatable

=back

=head1 OPTIONAL ARGUMENTS

=over