Using li93 to construct a molecular clock?

J.C Imbeault ah645 at Freenet.carleton.ca
Thu Nov 11 02:05:15 EST 1993



I'm in the middle of a prject where I have to construct a molecular clock using Li's program li93.  Not being a math, computer, or molecular evolution expert I haven't been able to figure how to do this. I have aligned my 
sequences and run them through li93 and gotten results (posted at the end...). Unfortunately I have no idea how
to interpret them or use them to construct a molecular clock.

Can anyone help?


          GAP272    NOFSRCH & NINDEX0    5    5  1.472
 CATEGORY                              ( i)      0             2             4
 i-FOLD DEGENERATE SITES IN SEQ1       (Li)  820.0         250.0         187.0
 i-FOLD DEGENERATE SITES IN SEQ2       (Li)  814.0         252.0         191.0
 AVERAGE    (Li = # OF i-FOLD SITES)   (Li)  817.0         251.0         189.0
 TRANSITIONAL SUBSTITUTIONS            (Pi)   23.5          32.2          25.2
 TRANSVERSIONAL SUBSTITUTIONS          (Qi)   15.0           1.9          11.1
 MEAN & S.E. OF TRANSITIONS PER SITE   (Ai) 0.03020.00633 0.14980.02871 0.16570.03650
 MEAN & S.E. OF TRANSVERSIONS PER SITE (Bi) 0.01870.00488 0.00780.00561 0.06220.01934
 MEAN & S.E. OF SUBSTITUTIONS PER SITE (Ki) 0.04890.00796 0.15760.02924 0.22800.04102

 $$$  COUNTING 1/3 OF A 2-FOLD DEGENERATE SITE AS SYNONYMOUS AND 2/3 AS NONSYNONYMOUS:

 Ks (Syn),    SE      0.29592   0.03882   # OF SITES 272.67
 Ka (Nonsyn), SE      0.04254   0.00676   # OF SITES 984.33

 $$$ Weighted Average:

 Ks (Syn),    SE      0.21889   0.02921
 Ka (Nonsyn), SE      0.04629   0.00742


Thank you!

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