distance between amino acids and sequences

Brian Foley btf at lanl.gov
Thu Apr 15 17:12:26 EST 1999

Lev Zhivotovsky wrote:
> Is there any computer program to get the distance matrix 
> for a set of amino acid sequences ?

	The PHYLIP programs, such as PROTDIST do this.


	You can choose from different distance measurements
such as PAM250 or Chemical Categories.

	The HIV Database has tools for calculating synonynous
vs nonsynonymous mutation rates at:


The syn:nonsyn ratio can give an idea of the selective
pressure on a coding region of DNA.  If all the observed
mutations are silent, it indicates that the amino acid
sequence must be conserved in order to maintain function.
If there is a high rate of nonsyn (amino acid changing)
mutations, it indicates the protein is being selected for
change, such as the HIV envelope protein mutating to evade 
the host immune system.

	Often times, DNA distances and protein distances
are not the same.  So it is wise to look at both, if you are
making phylogenetic inferences.

|Brian T. Foley               btf at t10.lanl.gov                       |
|HIV Database                 (505) 665-1970                         |
|Los Alamos, NM 87544  U.S.A.                                        |

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