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/