Ancestral Sequence Reconstruction with ancestral.pml

[MarStreicher]

Hey there, thanks for the grateful package!
Currently, I am working with the ancestral.pml command. You can see a part of my script here:

ml <- pml(tree_rooted, tips)
ml_opti <- optim.pml(sim_ml, optNni = TRUE, optBf = TRUE, optQ = TRUE,
                           optEdge = TRUE,
                           optRooted = TRUE, 
                           model = "HKY")
  
  sim <- ancestral.pml(ml_opti, "ml", return = "phyDat") 

I performed this command with different data sets and noticed that sometimes the root sequence was reconstructed and sometimes not. After reading the description, I do not find any hint for a reason.

Does anyone know in which cases the root reconstruction occurs and under which circumstances not?

Thank you very much!

[KlausVigo]

Dear @MarStreicher,

is it possible that you send me an example a of a tree / data where the error occured?

Kind regards,
Klaus

[MarStreicher]

Dear Klaus, the treefile is attached to this E-Mail. This is a phylogenetic tree of the Proboscidea based on their mitogenomes. Thank you very much! Kind regards, Marleen

…

On Mi, 21 Sep 2022 13:38:35 -0700 Klaus Schliep ***@***.***> wrote: Dear @MarStreicher, is it possible that you send me an example a of a tree / data where the error occured? Kind regards, Klaus -- Reply to this email directly or view it on GitHub: #131 (comment) You are receiving this because you were mentioned. Message ID: ***@***.***>

[KlausVigo]

Dear @MarStreicher,
I did not get the attachment, maybe send the alignment and trees to [email protected].
Thanks and kind regards,
Klaus