Hi, i m trying to align a fasta file(sequence.fasta) that contains 10 proteins.I want to use MUSCLE in order to do the alignment.I 've installed MUSCLE 3.6 and now im trying to have the right code.I m really new to all this stuff and my onle experience with perl is during the last 3 months so i need your help. MY Code: (or basically the code from bioperl.wiki) 

#!/ usr/bin/ perl
use strict;
use warnings;
use Bio::Tools::Run::Alignment::Muscle;
# Build a muscle alignment factory
my $factory =Bio::Tools::Run::Alignment::Muscle -> new(@params );
# Pass the factory a list of sequences to be aligned .
my $inputfilename = 'sequence.fasta ';
# $aln is a SimpleAlign object .
my $aln = $factory -> align ( $inputfilename );
# Perform a profile alignment on a MSA to include more seqs
my $alnfilename = 'sequence.fasta ';
my $seqsfilename = 'outfile ';
$aln = $factory -> profile ( $alnfilename , $seqsfilename );

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After trying to execute it, i get the message " Global symbol "@params" requires explicit package name". How do i define @params? I mean wthats the code thats missing? My task is to make a phylogentic tree from this fasta file, but the first step is to make the alignhment.The howtos don't really help me...

In reply to Aligning protein sequences using MUSCLE through Perl by DimitriC

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