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phylogenetic trees

Xavier Cousin xcousin at pasteur.fr
Wed Jun 5 08:32:37 EST 1996

hobert at FRODO.MGH.HARVARD.EDU (Oliver Hobert) wrote:
>Hey -
>I'm doing multiple sequence alignments with families of sequences from the
>worm genome project + cross-species homologs. Using GCG I get nice
>alignment but the phylogenetic trees I get with the "distances" and
>"growtree" command give very unreliable results (e.g. cross-species
>homologues appear in completely divergent branches). Does anybody know how
>to either get rid of this problem and/or whether there are any good other
>programs to have phylogenetic trees constructed ?
>Thanks a lot for a reponse,

Hello, if you get "nice alignment" it should be possible to build a reliable
What I suggest to you is to use ClustalW to obtain an alignment 
(alignment are usually "nicer" than with GCG PileUp) with the PHYLIP 
output option selected. You will then be able to build and check trees 
robustness by using various methods.

Read carefully the PYLIP instructions it's also a good introduction to

I presume that both programs (ClustalW and PHYLIP package) are available
via ftp.

As suggested by Dave Fitch in a previous answer, a theoretical knowledge
of phylogeny (and phylogeny inference methods) is very useful in this case of
study !!

Sincerly yours,


Xavier Cousin		xcousin at pasteur.fr

Unite des Venins	tel : (33 1) 45 68 86 30
Institut Pasteur	fax : (33 1) 40 61 30 57
25 rue du Dr Roux
75724 Paris cedex 15

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