[Bioperl-l] Problem in BioPerl. Help!

Roy Chaudhuri roy at colibase.bham.ac.uk
Fri Feb 24 15:51:46 UTC 2006

Praveen Raj wrote:
> 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.

Be careful with this. The .dnd files produced by ClustalW contain a 
Newick format guide tree- produced from pairwise-aligned sequences to 
guide the multiple alignment process. This should not be confused with a 
phylogenetic analysis, and the .dnd file is usually best ignored.

ClustalW can be used to produce a true phylogenetic tree from the 
alignment using the Neighbor-joining method (see the menus and 
documentation for details). This method produces files with a .ph or 
.phb extension (.phb if the tree is bootstrapped). I'm not sure if this 
process can be done using BioPerl, but it is possible to do using 
ClustalW's command line flags, so if you need to automate the process 
you could use Perl's system command. If you want to use BioPerl you can 
use the Phylip program neighbor to generate your tree directly from a 
SimpleAlign object, using the module 

Dr. Roy Chaudhuri
Bioinformatics Research Fellow
Division of Immunity and Infection
University of Birmingham, U.K.


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