RASA 2.3 is now available; please upgrade

Guy Hoelzer hoelzer at unr.edu
Fri Jun 11 13:08:52 EST 1999


RASA 2.3 is available; please upgrade from RASA 2.2

URL:
http://test1.bio.psu.edu/LW/rasatext.html

Some changes in RASA 2.3:

(1) Optimal outgroup analysis (Lyons-Weiler et al., 1998)
is (partly) automated. Combinations of outgroups input
sequence or combination of sequences (including inferred
ancestral sequences from other analyses) can be tested
using OOA.

(2) Bootstrap power and effect is implemented.
For this analysis, new algorithms analytically
determine each bootstrap pseudoreplicate's
regression parameters from the original RAS and E
pairwise similarity matrices. This increases the
speed over previous algorithms that bootstrapped
the sites, with no change in the result.

(3) Noise reduction is implemented as are algorithms
to export noise-reduced data;

(4) 2.3 uses the taxon variance ratio instead of
the taxon variance plot.  This allows comparison of
observed ratio to the sampling distribution of the ratio
as a test for 'significantly long' branch taxa;

(5) An improvement to the basic algorithm reduces the
computational time for each analysis;

(6) Some changes that should make the software more
stable on PPCs (please note the warnings on extensions);

and

(7) Minor cosmetic changes.

The new permutation null (which corrects for the inexactness
of the original test due to compositional biased) is still implemented.


Reference
Lyons-Weiler, J., G.A. Hoelzer and R.J. Tausch. 1998.
Optimal outgroup analysis. Biological Journal of the Linnean
Society 64:493-511




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