shift in annotated AA position

[antoine4ucsd]

Hi All, After importing codeml_tree from codon based alignment, I tried to add annotation of amino acid substitution inferred by joint probabilities with the following command: merged_tree <- ggtree::mask(codeml_tree, "joint_AA_subs", site) While I was able to visualize AA substitution on the tree, it does match the position in my original alignement...

Any thoughts about this apparent frameshift?

mydata.txt

[antoine4ucsd]

One additional finding while working on this issue. I think the discrepancies in AA positions may be due to the way gaps and amibiguities are handled... If I DO NOT check the 'Clean data' in PAML GUI (bottom right):

Then, read codeml will generate this error message:

BUT If I check the Clean Data in PAML, I can read the codeml files but the AA positions are not correct anymore... Any way to overcome this issue? Another method to track AA changes in the trees (maybe without PAML?)

thanks a lot!

Attached the codeml files and alignment codeml files IF I do not check the 'clean data' in PAML CL102Brooted-RAclockSE_mlc.txt CL102Brooted-RAclockSE_rst.txt CM102Brefm.phy.txt