Codon usage table

[SOMNATH CHINDHE]

Hello Experts,

I want to do pairwise dnds calculation using the yn00 program in paml. However, I want to add my own user codon usage table to this programme. Can I do it? If yes, please let me know.

Best regards, 

somnath

[Sishuo Wang]

Hi somnath,

I guess you might want to try directly editing the file src/tools.c.

See line 24 as follows, each number means the order or index of the corr animo acid in "AAs". For example. the first two 13s in line24 means the 1st two codons in the codon table, which are UUU and UUC, correspond to the 13+1=14th amino acid in "AAs" which is F (Phe). Maybe you can either add a new one or directly change an existing that you feel you are never going to use and then re-compile everything. I neither have tried it nor have been involved in developing paml so the above is just my guess. Hope it works.

Best,

Sishuo

[SOMNATH CHINDHE]

Dear Dr Shishuo Wang,

Thank you for providing information regarding the yn00 and codon usage table in PAML. I appreciate your help.

I have one more question for you. I was unable to locate the src/tools.c file. Do you have any information about this file?

Thank you for your time and consideration.

[Sishuo Wang]

Hi somnath,

i am not very sure i am using v4.10.3. have u tried "find path_to_paml -name tools.c" or "find -type f -exec grep ciliates -il {} \;"

Sishuo