Total number of sites in codeml result doesn't match the number of the phylip file and '"42 columns are converted into ??? because of the stop codon TAA'

[Chenyu Fan]

Hi,

I obtained the result from codeml using runmode = -2  seqtype = 1  CodonFreq = 2. In my input phylip file, the total number of sits is 29307. But in the result of codeml, the sum of number of N sites and S sites is less than 29307. In the meantime, when I run codeml, I get the information like "42 columns are converted into ??? because of the stop codon TAA". I am wondering if this case happens before? Does the wrong total number of sites in the codeml result have some connections with stop codons in phylip sequences?

pairwise comparison (Goldman & Yang 1994)
seq seq        N       S       dN       dS     dN/dS   Paras.
  2   1   9001.4   3139.6   0.0010   0.0003   3.1455   0.0025  19.8616   3.1455 -16013.324

Also, for the input phylip file of codeml, should I remove all the stop codons in sequences to make codeml work properly?

Best,

Chenyu Fan

 

[Ziheng]

yes, you should delete stop codons.

ziheng