[Bioperl-l] Problem in BioPerl. Help!
praveecbt at yahoo.co.in
Fri Feb 24 05:57:22 UTC 2006
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
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...
National Institute of Virology,
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