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reconstructions?</title></head><body>
<div><font color="#000000">i am studying the evolution of mimicry by
reconstructing ancestral states using the maximum likelihood criterion
with one-parameter Markov k-state model, implemented in
Mesquite</font>. on the phylogeny with ancestral reconstructions, when
i place the cursor over any of the internal nodes, the "trace
character" window lists all the character states and gives values
for each of those. for example, i have six character states for a
particular character, and a specific internal node shows the following
in the "trace character" window:</div>
<div><br></div>
<div>0:0.0002364</div>
<div>1:4.3728954467E-5</div>
<div>2:4.7586737726E-5</div>
<div>3:0.99771091*</div>
<div>4:0.00045689</div>
<div>5:4.7679802321E-5</div>
<div><br></div>
<div>are these numbers maximum likelihood scores? what do the '*' mean
in this case? i presume that the '*' denotes some kind of statistical
significance but i am not very sure. is it a significant value (at p <
0.05 or so) from a<font color="#000000"> maximum likelihood model for
a particular character state (state 3 in the above case) not being the
ancestral state at that node?</font> i am particularly confused
because if any single value in a given set of values is below ~0.85 or
so, the highest values that together make up >0.85 or so all get
the *. for example:</div>
<div><br></div>
<div>0:0.005565657</div>
<div>1:0.71353937*</div>
<div>2:0.00670567</div>
<div>3:0.26246278*</div>
<div>4:0.00614855</div>
<div>5:0.00056387</div>
<div><br></div>
<div>further, the highest (and single) value i get when i place the
cursor over any of the extant species is 1, without an asterisk. for
example, for a particular species:</div>
<div><br></div>
<div>5:1.0</div>
<div><br></div>
<div>if these are significant values of some sort, shouldn't the 1's
also have an asterisk in front of them?</div>
<div><br></div>
<div>i would appreciate any help with this, and thank you in
advance.</div>
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</pre></x-sigsep>
<div>Krushnamegh Kunte<br>
</div>
<div>FAS Center for Systems Biology<br>
Harvard University<br>
Cambridge, MA 02138, USA<br>
<br>
Office: (617) 384-9920<br>
Cell: (512) 577-1370<br>
Fax: (617) 495-2196<br>
Email: KKunte@cgr.harvard.edu or krushnamegh@gmail.com<br>
<br>
Academic Website:
http://www.bio.utexas.edu/grad/krushnamegh/Moorings/AcademicsHome.htm<br
>
General Website:
http://www.bio.utexas.edu/grad/krushnamegh/Moorings/index.htm</div>
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