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KlausVigo / phangorn

Phylogenetic analysis in R
http://klausvigo.github.io/phangorn/
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Ancestral Sequence Reconstruction with ancestral.pml #131

Open MarStreicher opened 2 years ago

MarStreicher commented 2 years ago

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 commented 2 years ago

Dear @MarStreicher,

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

Kind regards, Klaus

MarStreicher commented 2 years ago

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: https://github.com/KlausVigo/phangorn/issues/131#issuecomment-1254203608 You are receiving this because you were mentioned.

Message ID: @.***>

KlausVigo commented 2 years ago

Dear @MarStreicher, I did not get the attachment, maybe send the alignment and trees to klaus.schliep@gmail.com. Thanks and kind regards, Klaus