Best way to choose one orthologous sequences per species per Orthologous group

[LucieGL]

Is there any outfiles that would be handy to choose one orthologous sequences per species per orthogroup ? It is to make phylogenies with them. I could choose the longest but I fear that the longest sequeces could have additional domains compared to their in-paralogs Thanks!

[NINGCHINA]

I also have same need !

[davidemms]

Hi @LucieGL

Care should be taken with creating phylogenies from orthogroups with more than one gene per species since not all genes will be orthologs. There will not only be in-paralogs, but also genes in different species might be paralogs of one another. This means that a phylogeny for genes taken from such an orthogroup will, in general, be different from the species tree. I've updated the example on the github page to give a fuller example of this: https://github.com/davidemms/OrthoFinder#orthogroups-orthologs--paralogs

[davidemms]

I've got a script for extracting just sets of orthologs, I'll try and upload it this week.

[NINGCHINA]

Looking forward to it ！

2021年6月8日 下午7:31，David Emms @.***> 写道：

I've got a script for extracting just sets of orthologs, I'll try and upload it this week.

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[NINGCHINA]

Is there any outfiles that would be handy to choose one orthologous sequences per species per orthogroup ? It is to make phylogenies with them. I could choose the longest but I fear that the longest sequeces could have additional domains compared to their in-paralogs Thanks!

Here is an paper named "Comparative genomics of six Juglans species reveals diseaseassociated gene family contractions" , in the methods, the author describing how to get one species one orthologue. but it is hard for distant species. you can refer to it. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.14630

[NINGCHINA]

rthologs, I'll try and upload it this week.

just can't wait to see your script !

[LucieGL]

Many thanks for your help. In my case, the species are only distantly related. I might include all orthologous sequences at the end Best, Lucie

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De : zhang ning @.> Envoyé : vendredi 25 juin 2021 03:17 À : davidemms/OrthoFinder @.> Cc : LucieGL @.>; Mention @.> Objet : Re: [davidemms/OrthoFinder] Best way to choose one orthologous sequences per species per Orthologous group (#559)

Is there any outfiles that would be handy to choose one orthologous sequences per species per orthogroup ? It is to make phylogenies with them. I could choose the longest but I fear that the longest sequeces could have additional domains compared to their in-paralogs Thanks!

Here is an paper named "Comparative genomics of six Juglans species reveals diseaseassociated gene family contractions" , in the methods, the author describing how to get one species one orthologue. but it is hard for distant species. you can refer to it. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.14630

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/davidemms/OrthoFinder/issues/559#issuecomment-868281566, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AI3POOW5AYIPDNS32WB2AUDTUQUSPANCNFSM44PGNDSA.

[goshng]

Hi, I was wondering if the @davidemms updated the code with the script that could extract just sets of orthologs. I am also interested in getting one "representative orthologous" sequence per species from an orthofinder run. Thanks.

[NINGCHINA]

I did not find that scripts, but i also want find a way to get representative orthogroups.

Best Regards, Ning

2021年7月21日 下午5:08，Sang Chul Choi @.***> 写道：

Hi, I was wondering if the @davidemms https://github.com/davidemms updated the code with the script that could extract just sets of orthologs. I am also interested in getting one "representative orthologous" sequence per species from an orthofinder run. Thanks.

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[josephryan]

check out PhyloPyPruner https://pypi.org/project/phylopypruner/

[fantin-mesny]

Here is my approach: https://github.com/fantin-mesny/phylorep I hope it helps!