how to talk homology: part 2

Geoff Barton gjb at bioch.ox.ac.uk
Tue Nov 14 07:34:05 EST 1995

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
> 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

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 


Geoffrey J. Barton, Laboratory of Molecular Biophysics, University of
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

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