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The link from Anonymous Monk shows that Bio::Tools::Run::Alignment->new only takes one argument. The argument specifies the name of the output file of the alignment. So, you could do something like this...

#!/usr/bin/env perl

use strict;
use warnings;

use Bio::Tools::Run::Alignment::Muscle;

# Build a muscle alignment factory
my @params = ( -outfile_name => 'outfile.fa' );
my $factory = Bio::Tools::Run::Alignment::Muscle->new(@params);

# Pass the factory a list of sequences to be aligned .
my $inputfilename = 'sequence.fa';

# $aln is a SimpleAlign object .
my $aln = $factory->align( $inputfilename );

exit;
[download]

I grabbed some example data from here, and stored it in a file called sequence.fa

sequence.fa

>seq0
FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
>seq1
KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKKIEKFHSQLMRL
+ME LKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq2
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKKVEKLHGK
>seq3
MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK
>seq4
EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVSYEMRLFGVQKDNFALEHSLL
>seq5
SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKKIEKLTTLLMR
>seq6
FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKKLEKLSSTLLRSI
>seq7
SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKKMEKLNNIFF
>seq8
SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq9
KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
>seq10
FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKKMEK
[download]

When the script is running you should see some output from muscle.

Muscle Output

MUSCLE v3.8.31 by Robert C. Edgar

http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

sequence 11 seqs, max length 106, avg  length 67
00:00:00      1 MB(0%)  Iter   1  100.00%  K-mer dist pass 1
00:00:00      1 MB(0%)  Iter   1  100.00%  K-mer dist pass 2
00:00:00      2 MB(0%)  Iter   1  100.00%  Align node
00:00:00      2 MB(0%)  Iter   1  100.00%  Root alignment
00:00:00      2 MB(0%)  Iter   2  100.00%  Refine tree
00:00:00      2 MB(0%)  Iter   2  100.00%  Root alignment
00:00:00      2 MB(0%)  Iter   2  100.00%  Root alignment
00:00:00      2 MB(0%)  Iter   3  100.00%  Refine biparts
00:00:00      2 MB(0%)  Iter   4  100.00%  Refine biparts
00:00:00      2 MB(0%)  Iter   5  100.00%  Refine biparts
00:00:00      2 MB(0%)  Iter   6  100.00%  Refine biparts
[download]

When the script finishes you should see that the outfile.fa file was created and it should contain the aligned sequences.

outfile.fa

>seq9
---KNWEDFEIAAENMYMANPQNCRYTMKYVHSKGHILLKMSDNVKCVQYRAENMPDLKK
-----------------------------------------------
>seq7
----SWEEFVERSVQLFRGDPNATRYVMKYRHCEGKLVLKVTDDRECLKFKTDQAQDAKK
MEKLNNIFF--------------------------------------
>seq8
----SWDEFVDRSVQLFRADPESTRYVMKYRHCDGKLVLKVTDNKECLKFKTDQAQEAKK
MEKLNNIFFTLM-----------------------------------
>seq10
--FDSWDEFVSKSVELFRNHPDTTRYVVKYRHCEGKLVLKVTDNHECLKFKTDQAQDAKK
MEK--------------------------------------------
>seq6
--FTNWEEFAKAAERLHSANPEKCRFVTKYNHTKGELVLKLTDDVVCLQYSTNQLQDVKK
LEKLSSTLLRSI-----------------------------------
>seq5
----SWEEFAKAAEVLYLEDPMKCRMCTKYRHVDHKLVVKLTDNHTVLKYVTDMAQDVKK
IEKLTTLLMR-------------------------------------
>seq4
------EEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVVS-YEMRLFGVQKD
NFALEHSLL--------------------------------------
>seq0
--FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKK
IEKF-------------------------------------------
>seq1
-KYRTWEEFTRAAEKLYQADPMKVRVVLKYRHCDGNLCIKVTDDVVCLLYRTDQAQDVKK
IEKFHSQLMRLMELKVTDNKECLKFKTDQAQEAKKMEKLNNIFFTLM
>seq2
EEYQTWEEFARAAEKLYLTDPMKVRVVLKYRHCDGNLCMKVTDDAVCLQYKTDQAQDVKK
VEKLHGK----------------------------------------
>seq3
-MYQVWEEFSRAVEKLYLTDPMKVRVVLKYRHCDGNLCIKVTDNSVCLQYKTDQAQDVK-
-----------------------------------------------
[download]

In reply to Re: Aligning protein sequences using MUSCLE through Perl by kevbot
in thread Aligning protein sequences using MUSCLE through Perl by DimitriC

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