[Bioperl-l] Re: tcoffee tests in BioPerl

[cedric.notredame]

Dear all,

> It seems to me  that since version 1.34 is most probably newer than
> versions used when the  test were created, the way TCoffee orders
> sequences in the alignment might have changed. In fact, I did not find
> from the program documentation anything that would make me expect that
> the output sequences should be in any particular order. I'll cc: this
> mail to Cedric to get his comment on this.

t_coffee uses the same default as clustalw: It outputs the sequences in
the order they get aligned, so that the msa itself gives a rough
estimation of some phylogenetic relations. Therfore, if the estimation of
the sequences distances changes a little ( as happened before v1.34) the
tree topology can change as well. 

Personnaly I do not like this so much but I kept it because it is the
default of ClustalW. However, that can be changed using -outorder=input
rather than the default '-outorder=aligned.'
This flag is fully compatible with ClustalW. It is documented but I agree
that a mention in the FAQ might have helped :-). 

In any case, congratulations for all the work you guys are puting in this
stuff. Do not hesitate to get back to me if you have any 
question/suggestion, I will be really happy to help.

Cheers,

Cedric

> If only the order has changed, the percentage_identity() of the
> alignment should be the same even in older versions. Tests 10 and 12
> give the integer values 41 and 47 before and after adding the new
> sequence.
> 
> Jason/Peter, could you do 'cvs update' and see if these %identity
> values hold even with the t_coffee versions you are using?
> 
> I ran the clustalw and tcoffee tests under bioperl-07 which I have not
> updated and got identical results. It was a relief to find get an
> extra confirmation that I have not messed up anything in the bioperl
> alignment code.
> 
> If everything is as I suspect, it is easy enough change the tests from
> checking a name of the sequence in a given position in the alignment
> (which conflict the data encapsulation principle!) to comparing the
> number sequences in the alignment.
> 
> 
>         -Heikki
> 
> 
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
>