Im trying to align a fasta file (sequence.fasta) using MUSCLE through Perl,
and i get this very annoying message :
Can't call method "align" on an undefined value at C:\perlscripts\new1.pl line 8
What might be the problem???
#!/ usr/bin/ perl 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 ); use strict ;