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<div><font face="Courier New">Hi there,</font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">I'm getting some errors when trying to
run Baseml.pm I've checked the documentation and these should be
valid parameter values for runmode, Mgene, and fix_kappa. Also,
it's not locating the method "tree" in Baseml.pm - I
couldn't find it in there either. Should I just use
$codeml->tree($tree)?</font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">Thank you in advance for your
help.</font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">Alisha</font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">-------------------- WARNING
---------------------<br>
MSG: parameter runmode specified value 0 is not recognized, please see
the documentation and the code for this module or set the
no_param_checks to a true value<br>
---------------------------------------------------<br>
<br>
-------------------- WARNING ---------------------<br>
MSG: unknown parameter Mgene will not set unless you force by setting
no_param_checks to true<br>
---------------------------------------------------<br>
<br>
-------------------- WARNING ---------------------<br>
MSG: parameter fix_kappa specified value 0 is not recognized, please
see the documentation and the code for this module or set the
no_param_checks to a true value</font></div>
<div><font
face="Courier New">---------------------------------------------------</font
></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">Can't locate object method "tree"
via package "Bio::Tools::Run::Phylo::PAML::Baseml" at
batch_basemlpaml_simcon.pl line 77, <GEN1> line 1.</font><br>
<font face="Courier New"></font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New">Here's my code sample...</font></div>
<div><font face="Courier New">my $alignio = new Bio::AlignIO(-format
=> 'fasta',</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab>-file => $datafile);<x-tab>
</x-tab></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab>my $aln = $alignio->next_aln;</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab>if($aln){</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab> </x-tab>my
$baseml = new Bio::Tools::Run::Phylo::PAML::Baseml();</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('runmode', 0);<x-tab>
</x-tab>## user provided tree file</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('model',
4);<x-tab>
</x-tab><x-tab> </x-tab>## 0
JC 4 HKY85</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('Mgene', 0);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('fix_alpha', 1);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('alpha', 0);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('fix_kappa', 0);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('kappa', 2);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('fix_rho', 1);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('rho', 0);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->set_parameter('cleandata',1);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>print $baseml->executable(), " is
baseml\n";</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->alignment($aln);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab> </x-tab>my
$treefile = "msy.tre";</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab> </x-tab>my
$treein = Bio::TreeIO->new(-format => 'newick',-file =>
$treefile);</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab> </x-tab>my
$tree = $treein->next_tree;</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab><x-tab>
</x-tab></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab> </x-tab>##
this isn't working and I can't find this method in the baseml
doc</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>$baseml->tree($tree);</font></div>
<div><font face="Courier New"><br></font></div>
<div><font
face="Courier New"><x-tab>
</x-tab><x-tab>
</x-tab>etc.</font></div>
<div><font
face="Courier New"><x-tab>
</x-tab>}</font></div>
<div><font face="Courier New"><br></font></div>
<div><font face="Courier New"><br></font></div>
<div><br></div>
<x-sigsep><pre>--
</pre></x-sigsep>
<div>Alisha Holloway<br>
<br>
Postdoctoral Fellow<br>
Section of Evolution & Ecology<br>
3347 Storer Hall<br>
University of California<br>
Davis, CA 95616<br>
<br>
530-754-9551 Office<br>
512-297-3958 Cell<br>
530-752-1449 Fax</div>
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