Hello Klaus,
I would like to access the probability values for every site in my alignment. I cannot access the probabilities for every site within my alignment with the command
anc.ml = ancestral.pml(fit, "ml", return = "phyDat") or anc.ml = ancestral.pml(fit, "ml", return = "probs")
It appears when I reference one of the ancestral sequences as a result of the above command (return = "probs"), I only get the site pattern probabilities instead of all the probabilities.
anc.ml$62
I know this because my alignment has approximately 800 sites whereas I get around 190 sites, which is the same number as my site patterns. I also tried to directly output the probabilities to a file with the write.phyDat command but that has not worked for me. Thanks for the awesome program and I hope you can help me.
Cheers,
Xavier
Hello Klaus,
I would like to access the probability values for every site in my alignment. I cannot access the probabilities for every site within my alignment with the command
It appears when I reference one of the ancestral sequences as a result of the above command (return = "probs"), I only get the site pattern probabilities instead of all the probabilities.
I know this because my alignment has approximately 800 sites whereas I get around 190 sites, which is the same number as my site patterns. I also tried to directly output the probabilities to a file with the write.phyDat command but that has not worked for me. Thanks for the awesome program and I hope you can help me.
Cheers,
Xavier