[Bioperl-l] Problem in BioPerl. Help!

Praveen Raj praveecbt at yahoo.co.in
Fri Feb 24 05:57:22 UTC 2006

Dear sir,
           I have one problem in using Bioperl module 'Clustalw.pm'.
Clustalw creates SimpleAlign object as output,isn't it?.
  I successfully convert the object into 'clustal' and 'phylip' format using a
  file handler.
Sir, I want to make a newick format( for phylogenetic tree ) from the object itself.
But I know that Standalone Clustalw creates a newick file(.dnd extension) as an output along with 
the .aln file.
When I created a 'clustal' format and printed into a web page, it look like this;
  CLUSTAL W (1.83) Multiple Sequence Alignments
Sequence format is Pearson
Sequence 1: >gi|dengue2|           13 aa
Sequence 2: >gi|yellowfever|       13 aa
Start of Pairwise alignments
Sequences (1:2) Aligned. Score:  15
Guide tree        file created:   [\tXGgJDIuZZ\jmIerlkHz7.dnd]
Start of Multiple Alignment
There are 1 groups
  I don't know where the .dnd file(it's in newick format) is created.
It's not in the current directory.
Is there any method to specify the path for the .dnd file?
  I have gone through all the documentation provided with the BioPerl & clustalw.
How can I create a 'newick' output(.dnd file) format from a SimpleAlign object,created by Clustalw.pm?
  It's a great benefit for me, if you provide a solution for the same.
I can't move forward without a solution for this.
  So, Please reply...
                                    Thanking you,
                                                   Praveen Raj(student).
                                                   National Institute of Virology,   
                                                   Pune. India

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