Issue with multi-gene partition Model File in EPA-ng

[Thanu Chami]

Hi there,

I am currently using EPA-ng to place COI gene sequences on a large multi-gene backbone tree. The multi-gene tree was generated using RAxML-NG, with the model consisting of 27 models (for 27 genes in the partition file) generated from ModelTest-NG v0.1.7. I have passed the resulting [...]bestModel file from the evaluation run to EPA-ng. However, I am encountering an error stating: "Model string in provided file seems wrong."

Here is an overview of the steps I have taken:

1. Generated the multi-gene tree using RAxML-NG.
2. Used ModelTest-NG v0.1.7 to generate a file with 27 models corresponding to the 27 genes in the partition file.
3. Evaluated the model file and used the resulting [...]bestModel file in EPA-ng.

Despite these steps, the error persists. Could you please help me understand the reason behind this issue? Is it possible to use a multi-gene partition model file with EPA-ng?

I have attached the bestModel file I used for EPA-ng for your reference.

Thank you for your assistance.

Best regards,

Thanuja Fernando

[Alexandros Stamatakis]

Dear Fernando,

I would proceed as follows:

As you are trying to place COI sequences in a fixed tree it does not
make sense to pass the entire multi-gene MSA to EPA-NG. I don't think it
supports multiple partitions anyway but it also doesn't make any sense
to use the full MSA for placement if the sequences to be placed stem
froma very small region.

I would then take the backbone tree and just evaluate it for the CO1
region and then pass the respective parameters to EPA-NG for placement.

Hope that helps,

Alexis

On 01.08.24 04:16, Thanu Chami wrote:
> Hi there,
>
> I am currently using EPA-ng to place COI gene sequences on a large
> multi-gene backbone tree. The multi-gene tree was generated using
> RAxML-NG, with the model consisting of 27 models (for 27 genes in the
> partition file) generated from ModelTest-NG v0.1.7. I have passed the
> resulting [...]bestModel file from the evaluation run to EPA-ng.
> However, I am encountering an error stating: "Model string in provided
> file seems wrong."
>
> Here is an overview of the steps I have taken:
>

> 1. Generated the multi-gene tree using RAxML-NG.
> 2. Used ModelTest-NG v0.1.7 to generate a file with 27 models

> corresponding to the 27 genes in the partition file.

> 3. Evaluated the model file and used the resulting [...]bestModel file

> in EPA-ng.
>
> Despite these steps, the error persists. Could you please help me
> understand the reason behind this issue? Is it possible to use a
> multi-gene partition model file with EPA-ng?
>
> I have attached the bestModel file I used for EPA-ng for your reference.
>
> Thank you for your assistance.
>
> Best regards,
>
> Thanuja Fernando
>

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--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)