Is it possible to get a list of best-fitting models for a batch of MSAs?

[AndriiTarieiev]

Dear developers,

I would like to know whether it is possible to get a list of best-fitting models for a batch of MSAs. It would be very helpful for phylogenetic applications involving multiple different regions with different models.

Best regards, Andrii

[stamatak]

This tool that is based on ModelTest-NG could be helpful:

https://academic.oup.com/bioinformatics/article/35/10/1771/5132696

Alexis

On 20.12.23 17:26, AndriiTarieiev wrote:

Dear developers,

I would like to know whether it is possible to get a list of best-fitting models for a batch of MSAs. It would be very helpful for phylogenetic applications involving multiple different regions with different models.

Best regards, Andrii

— Reply to this email directly, view it on GitHub https://github.com/ddarriba/modeltest/issues/64, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGXB6TP333VFB5QV3YMGRLYKL7TPAVCNFSM6AAAAABA5AFQSGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA2TANZYGY2DAOA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- 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)

[dapogon]

Well, if you mean multiple MSAs for different regions of the exact same set of genomes (i.e., partitions), you might also want to take a look at PartitionFinder (https://www.robertlanfear.com/partitionfinder/). Best, D

---

David Posada CINBIO Universidade de Vigo 36310 Vigo Spain

Phone: +34 986 812038 Cell: +34 647 343300 Email: @.*** Web: http://darwin.uvigo.es

---

From: Alexis Stamatakis @.> Sent: Wednesday, December 20, 2023 4:36 PM To: ddarriba/modeltest @.> Cc: Subscribed @.***> Subject: Re: [ddarriba/modeltest] Is it possible to get a list of best-fitting models for a batch of MSAs? (Issue #64)

This tool that is based on ModelTest-NG could be helpful:

https://academic.oup.com/bioinformatics/article/35/10/1771/5132696https://urldefense.com/v3/__https://academic.oup.com/bioinformatics/article/35/10/1771/5132696__;!!D9dNQwwGXtA!TAkAeJnjN9aSCTmywxXHYMz9mVtebtStAByGcgKBJtZ2yym1F80nSeOpd15U_IPdKgeBpP1qyI-qSxfJq-pDIbo-$

Alexis

On 20.12.23 17:26, AndriiTarieiev wrote:

Dear developers,

I would like to know whether it is possible to get a list of best-fitting models for a batch of MSAs. It would be very helpful for phylogenetic applications involving multiple different regions with different models.

Best regards, Andrii

— Reply to this email directly, view it on GitHub https://github.com/ddarriba/modeltest/issues/64https://urldefense.com/v3/__https://github.com/ddarriba/modeltest/issues/64*3E__;JQ!!D9dNQwwGXtA!TAkAeJnjN9aSCTmywxXHYMz9mVtebtStAByGcgKBJtZ2yym1F80nSeOpd15U_IPdKgeBpP1qyI-qSxfJqx7I2A_I$, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGXB6TP333VFB5QV3YMGRLYKL7TPAVCNFSM6AAAAABA5AFQSGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA2TANZYGY2DAOAhttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAGXB6TP333VFB5QV3YMGRLYKL7TPAVCNFSM6AAAAABA5AFQSGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA2TANZYGY2DAOA*3E__;JQ!!D9dNQwwGXtA!TAkAeJnjN9aSCTmywxXHYMz9mVtebtStAByGcgKBJtZ2yym1F80nSeOpd15U_IPdKgeBpP1qyI-qSxfJq9JV1-BN$. You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- 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.grhttps://urldefense.com/v3/__http://www.biocomp.gr__;!!D9dNQwwGXtA!TAkAeJnjN9aSCTmywxXHYMz9mVtebtStAByGcgKBJtZ2yym1F80nSeOpd15U_IPdKgeBpP1qyI-qSxfJq9fvqhB7$ (Crete lab) www.exelixis-lab.orghttps://urldefense.com/v3/__http://www.exelixis-lab.org__;!!D9dNQwwGXtA!TAkAeJnjN9aSCTmywxXHYMz9mVtebtStAByGcgKBJtZ2yym1F80nSeOpd15U_IPdKgeBpP1qyI-qSxfJq5DxOJfN$ (Heidelberg lab)

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/ddarriba/modeltest/issues/64*issuecomment-1864692715__;Iw!!D9dNQwwGXtA!TAkAeJnjN9aSCTmywxXHYMz9mVtebtStAByGcgKBJtZ2yym1F80nSeOpd15U_IPdKgeBpP1qyI-qSxfJq0GeSWHK$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AE4VEEWRF3QH4C5BZ5W7NCTYKMAXNAVCNFSM6AAAAABA5AFQSGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRUGY4TENZRGU__;!!D9dNQwwGXtA!TAkAeJnjN9aSCTmywxXHYMz9mVtebtStAByGcgKBJtZ2yym1F80nSeOpd15U_IPdKgeBpP1qyI-qSxfJqwgQAGaj$. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[AndriiTarieiev]

Thank you!