TR_SoftParsMap

See also: SoftParsMap and NOTUNG evaluations.

------ Forwarded Message
From: "David A. Liberles" <liberles@uwyo.edu>
Date: Tue, 15 Sep 2009 18:32:47 -0500
To: <dstanzi@asu.edu>
Cc: <annesyl@uwyo.edu>
Subject: iPLANT

Hi,

Anne Sylvester (a colleague at University of Wyoming) suggested that I
contact you about a resource you are setting up for the iPLANT
initiative. We previously put together a gene tree/species tree
reconciliation package called SoftParsMap and are currently revising it
and working on a model-based extension to circumvent the known problems
of parsimony (eg branch length independence and multiple event
simplifications) based upon birth-death models using a Weibull
distribution. We have also previously put together (and are doing so
again) a pipeline for gene family database construction, detection of
positive selection in gene trees, and gene tree/species tree
reconciliation. Anyway, I attach some papers describing what we have
done. Please let me know if any of this is useful and if so, I welcome
the possibility of collaborating. Best wishes,

David Liberles
Department of Molecular Biology
University of Wyoming

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