[Bioperl-l] Representation of phylogenetic trees

[Jutta Buschbom]

Hi!

Thank you very much for your suggestions and comments! They were 
really helpful and answered my question. David described exactly what 
my problem was. I had read the perldocs and knew the methods that I 
wanted to apply, but didn't know the keys that would allow me to 
address specific attributes of an object, in my case its name 
('_id'). Marc's suggestion of using Data::Dumper, solved that. Plus I 
got a better idea how my tree looks like after it has vanished into 
the variable $tree.

Here a side remark on bptutorial.pl, since Marc suggested it: it 
doesn't work on my system (the installation of bioperl otherwise did 
seem to go very smoothly). Here is the error message that I get, 
maybe it is of interest to you:

~/Programs/bioperl-1.0.2> perl -w bptutorial.pl 100 Bio::Tools::Genscan
Can't locate LWP/UserAgent.pm in @INC (@INC contains: 
/usr/lib/perl5/5.6.1/ppc-linux /usr/lib/perl5/5.6.1 
/usr/lib/perl5/site_perl/5.6.1/ppc-linux 
/usr/lib/perl5/site_perl/5.6.1 /usr/lib/perl5/site_perl .) at 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm line 86.
BEGIN failed--compilation aborted at 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm line 86.
Compilation failed in require at 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/NCBIHelper.pm line 82.
BEGIN failed--compilation aborted at 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/NCBIHelper.pm line 82.
Compilation failed in require at 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/GenBank.pm line 112.
BEGIN failed--compilation aborted at 
/usr/lib/perl5/site_perl/5.6.1/Bio/DB/GenBank.pm line 112.
Compilation failed in require at bptutorial.pl line 2565.
BEGIN failed--compilation aborted at bptutorial.pl line 2565.

Again, thanks a lot for your help!

Best wishes,

Jutta