Question: Trouble in running Baseml
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gravatar for Biocode_user
4.3 years ago by
Biocode_user10
Sweden
Biocode_user10 wrote:

Hello,
I'm trying to do a nucleotide substitution analysis using a very simple model like Jukes and Cantor. I have a set of transcripts assembly and based on expression I have chosen the representative component of each  and did a reciprocal blastn on the  nucleotide sequences which is been jotted down from previous step. I did a pairwise alignment with clustalw for them. I have the alignment file in fasta format and now i'm trying to apply a simple nucleotide substitution model to proceed for further analysis. I'm using the perl wrapper for baseml and have the latest version of PAML and Bioperl installed.
I'm attaching the script that i'm trying to use and the error which i get. It would be greatly appreciable if someone could help on the same.
#!/usr/bin/perl -w
        use Bio::Tools::Run::Phylo::PAML::Baseml;
        use Bio::AlignIO;
        use Data::Dumper;
        my $alignio = Bio::AlignIO->new(-format => 'fasta',
                     -file   => $ARGV[0]);
       
        my $aln = $alignio->next_aln;
        my $baseml = Bio::Tools::Run::Phylo::PAML::Baseml->new();
        $baseml->alignment($aln);
        $baseml->set_parameter("runmode",2);
        $baseml->set_parameter("model",0);
        $baseml->set_parameter("noisy",9);
        $baseml->set_parameter("verbose",1);
        my ($rc,$parser) = $baseml->run();
        my $result = $parser->next_result; 
        my $MLmatrix = $result-> get_MLmatrix();
        print Dumper($MLmatrix);

Error
Can't call method "get_MLmatrix" on an undefined value at extract_base_test.pl line 27, <GEN1> line 6

rna-seq paml • 1.3k views
ADD COMMENTlink written 4.3 years ago by Biocode_user10
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