Estimation of rough substitution rate using codeml

[Manohar Singh Bisht 2110105]

Hi, 

I am running codeml on my amino acids alignments to calculate the rough substitution time which can later be used to find rgene_gamma to draw divergence tree. However, I couldn't able to locate the subsitution rate in the codeml output (file mlc)

PS: I am using PAML v4.8

Thanks

[Sishuo Wang]

Dear manohar,

I guess you should fix the date in the species tree file by "@1.1" for example instead of a range ">1<10" for that purpose. Also you may wish to note the version issue, perhaps work only for <4.9 version. see the following discussion

https://groups.google.com/g/pamlsoftware/c/Awc2iQ5QK5Y/m/hySQQa3lDAAJ

best,

sishuo

[Sishuo Wang]

Dear manohar,

following my last reply, so if your date is >1<10, then you can fix it at 5.5 by "@5.5", a toy example of your newick-formatted species tree file:

((a,b),c)'@5.5';

best,

sishuo