<P>Hi, all:</P>
<P> This is my first time post, thank you for your attention and any suggestion is greatly appreciated.</P>
<P>I just wonder if all modules of bioperl-run can work properly on wondows XP system. I tried ClustalW.pm, ProtPars.pm and ProtDist.pm. ClustalW module works fine after I copy clustalw.exe into my working folder. But ProtPars and ProtDist modules not work even if ProtPars.exe and ProtDist.exe works fine in my woking folder. Any suggestions? Thank you so much.<BR> <BR> <BR>Attached:<BR>A. Steps I took to install Bioperl-run:<BR>1. download bioperl-run-1.4 (current_run_stable.tar.gz) from<BR><A href="http://www.bioperl.org/Core/Latest/index.shtml" target=_blank>http://www.bioperl.org/Core/Latest/index.shtml</A>.<BR>2. Copy current_run_stable.tar.gz to my folder /bioperl_run and extract<BR>this gz file.<BR>3. Copy \bioperl_run\bioperl-run-1.4\Bio\Tools\Run (folder) to<BR>C:\Perl\site\lib\Bio\Tools and
replace the old folder Run, so that in<BR>current Run folder there are many new modules that I wish to use such as<BR>Alignment::TCoffee.pm.<BR></P>
<P>B. My code:</P>
<P>use Bio::Tools::Run::Phylo::Phylip::ProtPars;<BR>my $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(idlength=>30,threshold=>10); <BR>my $tree = $tree_factory->run("./folder/file.phy");</P>
<P>C. Error message:</P>
<P>'protpars.exe' is not recognized as an internal or external command,<BR>operable program or batch file.</P>
<P>------------- EXCEPTION -------------<BR>MSG: Protpars did not create treefile correctly<BR>STACK Bio::Tools::Run::Phylo::Phylip::ProtPars::_run C:/Perl/site/lib/Bio/Tools/<BR>Run/Phylo/Phylip/ProtPars.pm:348<BR>STACK Bio::Tools::Run::Phylo::Phylip::ProtPars::run C:/Perl/site/lib/Bio/Tools/R<BR>un/Phylo/Phylip/ProtPars.pm:279<BR>STACK toplevel Align_from_db.pl:169</P><BR>
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