[Bioperl-l] PAML problem

Du, Peng du at ibio.jp
Tue Jun 26 21:28:00 EDT 2012

Hi everyone,

I am using bioperl to parse paml output, and I saw this

------------- EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Unknown format of PAML output did not see seqtype
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::Tools::Phylo::PAML::_parse_summary
STACK: Bio::Tools::Phylo::PAML::next_result
STACK: main::cal_dn_ds dn_ds.pl:131
STACK: dn_ds.pl:44

I googled and found that, it was caused by PAML version
incompatibility. I tried 3.13, 3.14, 4.1, 4.2, 4.5 and none of them
worked. Could someone tell me which version is fine?

My bioperl version is 1.006001.  Thank you very much.


Peng Du
Graduate School of Information Science and Technology, Hokkaido University
Kita 14 Nishi 9 Kita-ku, Sapporo, Japan  060-0814
Email: du at ibio.jp Tel: +81 80 3268 9713

More information about the Bioperl-l mailing list