[Mesquitelist] likelihood reconstruction of CHANGES as well as states
david.fitch at nyu.edu
Thu Aug 14 07:16:48 PDT 2008
Dear Mesquite Users/Designers,
For a matrix of categorical (discrete) binary characters, how does
one output a table that details the likelihood reconstruction of
character-state CHANGE PROBABILITIES ("losses" and "gains") in each
character and each branch?
I see that Mesquite can output a table of the probabilities of HAVING
a particular state at each branch for each character (Analysis >
TraceAllCharacters). And I see that Mesquite can output a table of
changes occurring across a (or many) tree(s) for ONE particular
character at a time (Taxa&Trees > SummarizeStateChangesOverTrees),
which apparently depends on the "Likelihood Decision Threshold".
However, I cannot figure out how to output a table of CHANGE
PROBABILITIES for EACH branch for EACH character.
In the table I envision, for example, each character would be
represented by a row.
Each branch (node) would be represented by a pair of columns:
the 1st column with the number of (or probability of) gains,
the 2nd column with the number of (or probability of) losses.
Any ideas would be very welcome!
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~ ~ - -
~ David H. A. Fitch ~ \ / / /
~ Associate Professor ~ \/ / /
~ Department of Biology ~ \ / /
~ New York University ~  / /
~ Main Building, Room 1009 ~ \ / /
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