search

amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
385 stars 64 forks source link

how many sites per bootstrap replicate are sampled? #134

Closed goeckeritz closed 2 years ago

goeckeritz commented 2 years ago

Hi Alexey,

Apologies if this is a dumb question, but is there a way to know how many sites are sampled from an MSA to construct each bootstrap?

I'm trying to calculate confidence intervals for a date estimate using the different branches lengths for each bootstrap replicate, but to do that need to know the number of sites for each bootstrap tree.

Thanks so much in advance! Kindly, Charity

stamatak commented 2 years ago

The number of sites in each BS replicate is by definition equal to the number of sites in the original alignment.

Alexis

On 17.01.22 23:11, Charity Goeckeritz wrote:

Hi Alexey,

Apologies if this is a dumb question, but is there a way to know how many sites are sampled from an MSA to construct each bootstrap?

I'm trying to calculate confidence intervals for a date estimate using the different branches lengths for each bootstrap replicate, but to do that need to know the number of sites for each bootstrap tree.

Thanks so much in advance! Kindly, Charity

— Reply to this email directly, view it on GitHub https://github.com/amkozlov/raxml-ng/issues/134, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGXB6V4QRGFIOS3W74KIGDUWSAWTANCNFSM5MFS2T7Q. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas

www.exelixis-lab.org

amkozlov commented 2 years ago

Hi Charity,

please see the answer above. Also, please use our google group for general questions:

https://groups.google.com/g/raxml

Best, Alexey

goeckeritz commented 2 years ago

Hi Alexis & Alexey,

Thanks so much for the response -- makes sense. Sorry about posting in a weird spot! I'll use the google groups from now on!

Kindly, Charity

amkozlov commented 2 years ago

perfect, no problem :)

so I'm closing this issue then.