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chaoszhang / ASTER

Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)
GNU Affero General Public License v3.0
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Getting Quartet support values #10

Closed bvs closed 1 year ago

bvs commented 1 year ago

Hi,

Thank you for developing this wonderful tool. I successfully ran the ASTRAL-Pro2 multiple times on gene trees with paralogs. However, I cannot get quartet support values (q1, q2 and q3) like in ASTRAL-III. I tried with the -u flag, but still, I am not getting q values. Is there a to get q values?

Best, Suresh

chaoszhang commented 1 year ago

Hi Suresh,

Thanks for using our tools. You can get f1, f2, and f3 using -u 2 option, then q1 = f1 / (f1 + f2 + f3), ditto for q2 and q3.

If you want me to update ASTRAL-Pro2 to output q1, q2 and q3, please let me know. :)

Best, Chao

bvs commented 1 year ago

Dear Chao,

Thank you for the information. It would be great if you can update the ASTRAL-Pro2 to directly output the q values as I need to compute species trees several times.

Best, Suresh

On Wed, Feb 15, 2023 at 4:46 PM Chao Zhang @.***> wrote:

Hi Suresh,

Thanks for using our tools. You can get f1, f2, and f3 using -u 2 option, then q1 = f1 / (f1 + f2 + f3), ditto for q2 and q3.

If you want me to update ASTRAL-Pro2 to output q1, q2 and q3, please let me know. :)

Best, Chao

— Reply to this email directly, view it on GitHub https://github.com/chaoszhang/ASTER/issues/10#issuecomment-1431575656, or unsubscribe https://github.com/notifications/unsubscribe-auth/AADGTQ7POCJH2SIYSCHXPN3WXT23ZANCNFSM6AAAAAAU4XL4AQ . You are receiving this because you authored the thread.Message ID: @.***>

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Dr. Bonthala Venkata Suresh, Ph.D., MRSB Heinrich-Heine-Universität Quantitative Genetik & Genomik der Pflanzen Universitätsstraße 1 40225 Düsseldorf

Email: @.***

Google Scholar https://scholar.google.co.uk/citations?user=xqcsfL0AAAAJ&hl=en ResearchGate https://www.researchgate.net/profile/Venkata_Suresh_Bonthala

chaoszhang commented 1 year ago

Sure. I will let you know when it is done.

chaoszhang commented 1 year ago

Please try ASTRAL-Pro2 v1.14.1.3.

bvs commented 1 year ago

Dear Chao,

Thank you for the quick update.

Best, Suresh

JGLAHE commented 1 year ago

Hi Chao,

I can't seem to find v1.14.1.3 in any of the changelogs?

Cheers

chaoszhang commented 1 year ago

The version v1.14.1.3 is specifically for ASTRAL-Pro. In general, if you find v1.14.x.x or above. This feature should already been implemented.