[BiO BB] PAML (baseml)

[Stefan Rensing]

Ryan,

the main_result.txt contains at its end some lines like this:

Substitution rate is per time unit
Gene  1:     0.023706 +- 0.002073
Gene  2:     0.061812 +- 0.005858

Nodes and Times
(JeffNode is for Thorne's multidivtime.  ML analysis uses ingroup data
only.)

Node   7 (Jeffnode  10) Time  10.15223 +- 0.94581
Node   8 (Jeffnode   9) Time   6.74960 +- 0.58392
Node   9 (Jeffnode   8) Time   4.17529 +- 0.27483
Node  10 (Jeffnode   7) Time   3.20000
Node  11 (Jeffnode   6) Time   2.34832 +- 0.20325

rates for 2 genes:     1  0.06181

Dunno if this helps; I have used PAML for calculation of divergence times.

Have you tried r8s? http://ginger.ucdavis.edu/r8s/
It offers a lot more options.

Best regards,
Stefan

Ryan Golhar wrote:

> Has anyone every used PAML for measuring substitution rates?  I'm using
> baseml to do this, however the documentation mentions NOTHING about how
> to interpret the output files.  
> 
> If anyone has used this I could sure you your help...
> 
> 
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-- 
Dr. Stefan Rensing, Group Leader Computational Biology
Plant Biotechnology, Faculty of Biology, University of Freiburg
Schaenzlestr. 1, D-79104 Freiburg, Fon: +49 761 203-6974, Fax: -6945
http://www.plant-biotech.net/  http://www.cosmoss.org/
stefan.rensing at biologie.uni-freiburg.de

"Mr. Musgrave, please don't interrupt me when I'm asking rhetorical
questions."