[BiO BB] PAML (baseml)

[Ryan Golhar]

Thanks Stefan.  My output actually looks like this.  This is from an
intron, and I'm trying to measure the substitution rate (Ki).  I'm
looking at this and not quite sure how to interpet these numbers.   What
is Ki?  I thought it would be 1.3471, but then what is 2.1629 (and
lnL?).   1.3471 seems a little high.  

BASEML (in paml 3.14beta, July 2003)  /tmp/ZBQQHmB5FA/FzTq4tS9qr  HKY85
ns = 2          ls = 645
# site patterns = 16
   39   32   96  100   20   34   60   16   17   37   28   32   39   39
26
   30

chick                                GTATATTCGA CGACCG
human                                AC..CGAGCT ..GTAT

Frequencies..
                                    T      C      A      G
chick                          0.3504 0.1690 0.2977 0.1829
human                          0.3194 0.1504 0.3426 0.1876

Average                        0.3349 0.1597 0.3202 0.1853

# constant sites:    256 (39.69%)
ln Lmax (unconstrained) = -1691.878455

Distances:HKY85 (kappa)  (alpha set at 0.00)
This matrix is not used in later m.l. analysis.

chick
human              1.3471( 2.1629)

stage 0: (1, 2);
lnL(ntime:  2  np:  3):  -1696.679873
   3..1     3..2
  0.99850  0.37679  2.25465


best tree: (1, 2);   lnL:  -1696.679873
(chick: 0.998497, human: 0.376793);

-----Original Message-----
From: Stefan Rensing [mailto:stefan.rensing at biologie.uni-freiburg.de] 
Sent: Friday, June 23, 2006 9:16 AM
To: golharam at umdnj.edu; The general forum at Bioinformatics.Org
Subject: Re: [BiO BB] PAML (baseml)


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."