RASA 2.2

[James Francis Lyons-Weiler]

Dear TAXACOM subscribers:

Please note that RASA version 2.2 software for measuring phylogenetic
signal and data analysis has been uploaded and can be downloaded
at the following URL as a binhexed, self-extracting archive:

http://loco.biology.unr.edu/archives/rasa/rasa.html

and by anonymous ftp at

        loco.biology.unr.edu (pub) (rasa)

This software (for Mac only) corrects a serious bug in the power&effect
analysis option in RASA 2.1.  Please pass this announcement along to any
user you may know who might not be a subscriber to TAXACOM.

RASA 2.2 also offers two null hypothesis formulations: the original,
analytical, equiprobable null and a new permutation null that provides a
better fit of the test to the student-t distribution.

Other features include:

a tool for the detection of otherwise cryptic long edge taxa, which cause
inconsistency of methods of tree-building.  This tool (the taxon variance
plot) was recently described in

        Lyons-Weiler, J., and G.A. Hoelzer. 1997.  Escaping from the
        Felsenstein Zone by detecting long branches in phylogenetic data.
        Molecular Phylogenetics and Evolution 8:375-384.

a test for the suitability of outgroup taxa for rooting trees, to be
described in

        Lyons-Weiler, J., G.A. Hoelzer and R.J. Tausch. 1998.  Optimal
        Outgroup Analysis. Biological Journal of the Linnean Society
        (in press).

new experimental treatments of phylogenetic data, including a type of
waveform analysis that reveals structure in biological sequences

        The software is menu-driven, with the following options
        (some not yet activated):

                2.1 File Menu
                        2.1.1 Open
                        2.1.2 Open Several
                        2.1.3 Open Results
                        2.1.4 Close
                        2.1.5 Save Results As
                        2.1.6 Export Modified Matrix
                        2.1.7 Print
                        2.1.8 Quit
                2.2 Analysis Menu
                        2.2.1 Signal Content
                        2.2.2 SC Recursive
                        2.2.3 Optimal Outgroup Analysis
                        2.2.4 Power and Effect
                        2.2.5 Colonization/Extinction Ratio
                        2.2.6 Character Compatibility
                        2.2.7 Signal Waveform
                2.3 Graphs
                        2.3.1 Regression
                        2.3.2 Taxon Variance Plot
                        2.3.3 Show Signal Waveform
                        2.3.4 Residual Plots
                        2.3.5 RASA Table
                        2.3.6 Show Data Matrix
                2.4 Data
                        2.4.1 Include/Exclude Taxa
                        2.4.2 Define Outgroup Taxa
                        2.4.3 Remove Invariant Characters
                        2.4.4 Remove APPARENT Autapomorphies
                        2.4.5 Recode Purines and Pyrimidines
                        2.4.6 Create Combined Data Matrix
                        2.4.7 Delete Noisy Characters
                2.5 Windows
                        2.5.1 Clear the Screen
                        2.5.2 Main Display
                        2.5.3 Help
                        2.5.4 References
                        2.5.5 Acknowledgements
                        2.5.6 Close All

        Please send questions to weiler at equinox.unr.edu