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            my ($filename) = fileparse($infile);
            my $outfile = file($subdir, $filename)->stringify;
            $new_ali->store($outfile);
        }
    }

}

__END__

=pod

=head1 NAME

prune-outliers.pl - Identify and discard outliers based on all-versus-all BLAST searches

=head1 VERSION

version 0.213470

=head1 USAGE

	prune-outliers.pl <indirs> [options]

=head1 REQUIRED ARGUMENTS

=over

=item <indirs>

Path to input directories containing ALI (or FASTA) files [repeatable argument].

=for Euclid: indirs.type: string
    repeatable

=back

=head1 OPTIONS

=over

=item --evalue=<n>

evalue threshold for a hit to be considered during the all-versus-all BLAST
searches [default: n.default].

=for Euclid: n.type: num
    n.default: 1e-10

=item --min-ident=<n> | --min_ident=<n>

Minimal identity value used for selecting sequences that match at least this
proportion in the all-versus-all BLAST searches [default: n.default]. An output
dir will be created by step of 0.1 between the min threshold and max threshold.

=for Euclid: n.type: num
    n.default: 0.3

=item --max-ident=<n> | --max_ident=<n>

Maximum percent value used for selecting sequences that match at least this
proportion in the all versus all BLAST searches [default: n.default]. An output
dir will be created by step of 0.1 between the min threshold and max threshold.

=for Euclid: n.type: num
    n.default: 0.8

=item --min-hits=<n> | --min_hits=<n>

Minimum number of hits in the all-versus-all BLAST searches required for a
sequence to be retained in the output file [default: n.default].

=for Euclid: n.type: num
    n.default: 10

=item --[no]guessing

[Don't] guess whether sequences are aligned or not [default: yes].

=item --version

=item --usage

=item --help

=item --man

Print the usual program information

=back

=head1 AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

=head1 CONTRIBUTORS

=for stopwords Amandine BERTRAND Loic MEUNIER

=over 4

=item *

Amandine BERTRAND <amandine.bertrand@doct.uliege.be>

=item *

Loic MEUNIER <loic.meunier@doct.uliege.be>

=back

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut