/usr/bin/protein_alignment_from_nucleotides is in roary 3.8.0+dfsg-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 | #!/usr/bin/env perl
package Bio::Roary::Main::GeneAlignmentFromNucleotides;
$Bio::Roary::Main::GeneAlignmentFromNucleotides::VERSION = '3.8.0';
# ABSTRACT: Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT
# PODNAME: protein_alignment_from_nucleotides
use Cwd qw(abs_path);
BEGIN { unshift( @INC, abs_path('./lib') ) }
BEGIN { unshift( @INC, abs_path('./t/lib') ) }
use Bio::Roary::CommandLine::GeneAlignmentFromNucleotides;
Bio::Roary::CommandLine::GeneAlignmentFromNucleotides->new(args => \@ARGV, script_name => $0)->run;
__END__
=pod
=encoding UTF-8
=head1 NAME
protein_alignment_from_nucleotides - Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT
=head1 VERSION
version 3.8.0
=head1 SYNOPSIS
Take in multi-FASTA files of nucleotides and align each file with PRANK or MAFFT
=head1 AUTHOR
Andrew J. Page <ap13@sanger.ac.uk>
=head1 COPYRIGHT AND LICENSE
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007
=cut
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