1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
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seqfile = PAML/alignment.phylip * sequence data file name
outfile = temp.out * main result file
verbose = 1 * 1: detailed output (list sequences), 0: concise output
icode = 0 * 0:universal code; 1:mammalian mt; 2-10:see below
weighting = 0 * weighting pathways between codons (0/1)?
commonf3x4 = 0 * use one set of codon freqs for all pairs (0/1)?
ndata = 1
* Genetic codes: 0:universal, 1:mammalian mt., 2:yeast mt., 3:mold mt.,
* 4: invertebrate mt., 5: ciliate nuclear, 6: echinoderm mt.,
* 7: euplotid mt., 8: alternative yeast nu. 9: ascidian mt.,
* 10: blepharisma nu.
* These codes correspond to transl_table 1 to 11 of GENEBANK.
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