Percent identity for numerous comparisons

Nicolas Le Nov=E8re lenov at pasteur.fr
Tue May 5 12:30:10 EST 1998



Elisa Eshbaugh wrote:

> Hello all and thanks to those who can make a suggestion...
> I am calculating %identity (amino acid and nucleotide) among 43
> different taxa representing 4 subfamilies of a gene family. This means
> that by the time I have done every possible pairwise comparison there
> will be hundreds. There's really no problem in doing this, but it kind
> of eliminates the potential for putting all the information in a nice
> little table. If I want to extract as much information as possible, but
> eliminate any less than necessary work, what might be some criteria for
> eliminating some of the comparisons?

I wrote a program which deals (as a side output) with the pairwise
identities(or similarities according to the matrix you choose). In the
output file,
you have every pairwise comparisons in a matrix and in a comumn format.
See at:
http://www.pasteur.fr/units/neubiomol/softwares.html

--
Nicolas Le Nov=E8re, Neurobiologie Mol=E9culaire, INSTITUT PASTEUR
25, rue du DR ROUX, 75724 Paris cedex
Ph: 33-(0)1-45-68-88-44, Fax: 33-(0)1-45-68-88-44, email: lenov at pasteur.fr
http://www.pasteur.fr/units/neubiomol/





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