computing pairwise ts/tv.

James Foster foster at cs.uidaho.edu
Fri Aug 19 11:56:01 EST 1994


Sudhir Kumar (IMEG at psuvm.psu.edu) wrote:
: Much of the discussion about transition/transversion ratios in this forum has
: been directed towards nucleotide sequence data that has more than 2 sequences.
:  To get an idea regarding ts/tv bias, we can also compute this ratio for every
: pair of sequences in the data.  In computer program MEGA, all pairwise ts/tv's
: can be computed in one run along with their standard errors.  In addition, one
: can also compute distances based only on transversional substitutions, if one
: suspects that transitional substitutions are close to saturation.  This can be
: done for most of the distance estimation methods available, such as the ones
: that do not require G+C-content to be equal to 50% and the ones that require
: more than 3 parameters for modelling the substitution patterns.
:                                                    Sudhir Kumar

How do I get a copy of MEGA?

--
James A. Foster					email: foster at cs.uidaho.edu
Laboratory for Applied Logic			Dept. of Computer Science
University of Idaho				www: http://www.cs.uidaho.edu/



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