several outgroup

[RozimovAkbarjon]

When I select multiple outgroup likely: (-o Seur-1,Seur-2). It is only including Seur-1 as an outgroup, but not including second sample. How can I include several outgroup?

[edgardomortiz]

Hi @RozimovAkbarjon ,

ONLY the first sample in an alignment is interpreted by most phylogenetic programs as the outgroup when estimating the phylogeny (the resulting tree will be rooted on that sample, check for example the option -o of IQTREE here: http://www.iqtree.org/doc/Command-Reference). Therefore, selecting more than a single sample as the outgroup will not have any effect on the resulting phylogeny.

As of now just a single outgroup can be selected, what would be the purpose of selecting several? Maybe I could add the option if it is justified.

Edgardo

[RozimovAkbarjon]

Hi Dr. Edgardo, Sounds alright to me. Thank you much for a quick response. Akbarjon Rozimov Ph.D student Fish Evolution and Genomics Group Key Laboratory of Zoological Systematics and Evolution Institute of Zoology, Chinese Academy of Sciences 1 Beichen West Road, Chaoyang, Beijing 100101, P.R. China

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On Thu, 9 Jan 2025 at 17:45 Edgardo M. Ortiz ***@***.***> wrote: Hi @RozimovAkbarjon <https://github.com/RozimovAkbarjon> , ONLY the first sample in an alignment is interpreted by *most* phylogenetic programs as the outgroup when estimating the phylogeny (the resulting tree will be rooted on that sample, check for example the option -o of IQTREE here: http://www.iqtree.org/doc/Command-Reference). Therefore, selecting more than a single sample as the outgroup will not have any effect on the resulting phylogeny. As of now just a single outgroup can be selected, what would be the purpose of selecting several? Maybe I could add the option if it is justified. Edgardo — Reply to this email directly, view it on GitHub <#53 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BC65JIPCWQZQQ6L6X5GMBBD2JZAKDAVCNFSM6AAAAABU3UEWDOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNZZGYYDMMJZGY> . You are receiving this because you were mentioned.Message ID: ***@***.***>