SI-Johanne Duhaime wrote:
>> Thank you for all the people that answered my question about "how to talk
> homology with pileup". Every body suggested me to use the program
> Distances. This give an idea about the homology between each two sets of
> sequences of the alignment.
> But what I am interessed in is to measure for each position of an alignment
> a kind of score of homology. If I have 20 aligned sequences where are the
> highlycon served regions and how much are they homologues? This is more or
> less the result of plotsimilary but in ascii terms.
> Is this sound correct for "to talk homology". And is there any program
> doing that?
>> Thank you again
>> Johanne Duhaime
> IRCM
>Duhaimj at ircm.umontreal.ca
You could try AMAS. This analyses multiple alignments on a
position by position basis. It gives a text and graphic
output of the analysis. It also allows you to subgroup
the sequences and look for similarities/differences between
sub-groups.
You can try the AMAS server via http://geoff.biop.ox.ac.uk/
or get a copy of the program by following the instructions in
ftp://geoff.biop.ox.ac.uk/README
Geoff.
--
Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of
Oxford,
Rex Richards Building, South Parks Road, Oxford OX1 3QU, U.K.
mailto:gjb at bioch.ox.ac.uk, Tel: +44 1865 275368, Fax: +44 1865 510454,
ftp://geoff.biop.ox.ac.uk,http://geoff.biop.ox.ac.uk
