4
1: DN HQ LI MI ML FI FL YF VM
5
2: QR ED EQ HR PA SN TP VI VL
6
3: GA KQ KE SG TA TN TS WL VA VF
7
4: HN HD PQ PH SP TK TM YH
11
Partitioning according to grantham.dat, for table 5 in Yang et al. (1998).
16
1: RH RK DE AG AP AS AT AV NI NS NT NY CG CF CS CW CY QL QP GS GW GV IL IM IF IS IT IV LM LF LP LS LW LV MT MV FS FY FV PS PT ST SW SY
21
Prepared by Wa Yang. This partitions amino acid changes into the
22
conserved changes (class 1 above) and radical changes (class 0, which
23
includes all the other changes). This partitioning is based on
24
charge. The list works on universal code. For mt code (icode = 1),
25
some of the pairs specified cannot really change between themselves in
26
one step and should be deleted. I did not check carefully and the
27
program simply ignores such pairs.
32
Notes for file format: The number on the first line is the number of
33
substitution types or omega's. This line is followed by as many lines
34
as the number of substitution types. The last line, not read by the
35
program, includes all amino acid pairs not mentioned before. If the
36
specified amino acid pair cannot change between themselves in one step
37
(by one codon-position difference), the pair is discarded, with a
38
warning message. To fit the "general" model, assigning an independent
39
w ratio for each one-step amino acid pair, put -1 at the start of the
40
file, and then the program will ignore the rest of the file and fit
41
the general model (see pages 1608-1609 in Yang et al. 1998).
45
Yang, Z., R. Nielsen and M. Hasegawa. 1998. Models of amino acid
46
substitution and applications to mitochondrial protein evolution.
47
Mol. Biol. Evol. 15:1600-1611.
added
removed
examples/mtCDNA/OmegaAA.dat
