read.hyphy input

[dikeledik]

Good day

I am trying to visualise amino acid substitution on the phylogenetic tree and cannot figure out how to produce the Ancestral sequences .nex file that is an input in the following command (I have the fasta and nwk file):

hy <- read.hyphy(nwk, ancseq, tipfas)

Which module/model do i use?

Thank you.

[spond]

Dear @dikeledik,

It appears that you are using an R function which was developed by someone other than us. As such, I cannot tell you what the expected input is. Do you have any further references?

Best,
Sergei

[dikeledik]

Thank you for your response Sergei, this is the reference i am using: https://yulab-smu.top/treedata-book/chapter5.html figure 5.9. The function is described here: https://rdrr.io/bioc/treeio/man/read.hyphy.html, and it allows for amino acid substitutions to be displayed on the tree