New Version of RASA

[Richard Zander]

A forward of notice of a new version of RASA.

---------
Richard H. Zander
Curator of Botany
Buffalo Museum of Science
1020 Humboldt Pkwy
Buffalo, NY 14211 USA
email: rzander at sciencebuff.org
voice: 716-895-5200 x 351



----- Original Message -----
From: "James Lyons-Weiler" <jfl8 at psu.edu>
To: "Richard Zander" <rzander>
Sent: Thursday, March 23, 2000 6:37 PM
Subject: please post
>
>
> ***********************************************
> ***  Software Update Announcement  ***
> ***********************************************
>
> RASA 2.4 for the Mac is now available.
>
> http://test1.bio.psu.edu/
>
> Changes from RASA 2.3
> - Improved the speed of the RASA core algorithm.
> - Added a gap-handling menu option.
> - Activated the 'View Signal Profile' option.
> - Added an option to save signal profile as PAUP (Nexus)
> exSets for easy noise reduction.  Signal profiles can
> still be saved as text for viewing in graphing software.
> - Added a list of studies that have used RASA.
> - RASA 2.4 should now 'background' with no trouble.
>
> RASA 2.4 is now more stable, especially Mac OS 8.5.1 and higher.
> Those experiencing problems with RASA 2.4 should avoid using
> superfluous extensions and office-manager type utilities while
> running RASA 2.4.
>
> As in RASA 2.3, the taxon variance comparison (used for detecting
> long branch taxa) is now made using a taxon variance ratio (Ftv).
> Although provided, users shouldn't worry about "significant levels"
> of Ftv's.  The assumed sampling distribution is valid for a limited case
> (equal frequencies of four-state characters).  Taxa (sequences) with
> high Ftv values when others have low Ftv values represent sequences
> on branches that need to be intercepted by further taxon sampling, or
> eliminated to reduce branch length heterogeneity.
>
> All other options, including
> * measuring phylogenetic signal of individual data sets (identifying noisy
> genes);
> * viewing the RASA regression and residual plots;
> * testing the suitability of given outgroup sequences;
> * detecting long branches;
> * identifying and removing noisy sites;
> * calculating phylogenetic signal power curves;
> * specifying the analytical or permutation-based null hypothesis;
> * calculating a colonization/extinction ratio; and
> * measuring signal for many  (e.g., simulated) data sets
>
> are, of course, still available.
>
> Papers describing two new options are under preparation
> bootstrap power and effect (for determining signal power curves)
> and noise reduction (for removing sites that reduce signal).
>
> Users should publish results from these two new analyses only after
contacting
> JLW
>
> jfl8 at psu.edu
>
>
> James Lyons-Weiler, PhD
> INSTITUTE OF MOLECULAR EVOLUTIONARY GENETICS
> Department of Biology
> 311 Mueller Laboraties
> The Pennsylvania State University
> University Park, PA 16802
> ph (814) 865-1034
> fax (814) 863-7336
> JFL8 at psu.edu
> http://test1.bio.psu.edu/
>
>