Adding branch length and bootstraps to a consensus tree

[npbhavya]

I was able to build a 100 trees with branch lengths using tutorial available. But when when I run the command to build a consensus tree to get the bootstrap values, the branch lengths are being saved as 1. Below is the command I ran,

raxmlHPC -m GTRGAMMA -J MRE -z RAxML_bootstrap.isolates53-raxml-GTRGAMMA-branchLength -n 53genomes_Wbranchlngths -k

Is there a way to build a consensus tree with bootstrap values and branch lengths.

Thank you, Bhavya

[stamatak]

The problem here is how to obtain the branch lengths.

One could either try to optimize the branch lengths on the multi-furcating consensus tree which RAxML can't do as it can only compute likelihoods on strictly binary trees. On the other hand one could try to compute some average over the branch lengths of the trees that are used to construct the consensus tree, but it's a bit unclear how to do this, maybe you can find some tool for post-analyzing Bayesian MCMC results that might be able to do this.

Why don't you just draw the support values on the best found ML tree instead?

Alexis

On 19.11.21 08:20, Bhavya Papudeshi wrote:

I was able to build a 100 trees with branch lengths using tutorial available. But when when I run the command to build a consensus tree to get the bootstrap values, the branch lengths are being saved as 1. Below is the command I ran,

raxmlHPC -m GTRGAMMA -J MRE -z RAxML_bootstrap.isolates53-raxml-GTRGAMMA-branchLength -n 53genomes_Wbranchlngths -k

Is there a way to build a consensus tree with bootstrap values and branch lengths.

Thank you, Bhavya

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-- 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

[npbhavya]

Thank you for the reply. I didn't consider using just the support values for the best found ML tree. How do I pick the best ML tree from the bootstrap tree output, would it just be the first or last one in this file?

Also, I am trying to visualise the tree with branch length and bootstrap values. So is there a way I can generate a Bewick file with both these values.

[stamatak]

All this can be found in the step by step tutorial here:

https://cme.h-its.org/exelixis/web/software/raxml/hands_on.html

Alexis

On 22.11.21 07:12, Bhavya Papudeshi wrote:

Thank you for the reply. I didn't consider using just the support values for the best found ML tree. How do I pick the best ML tree from the bootstrap tree output, would it just be the first or last one in this file?

Also, I am trying to visualise the tree with branch length and bootstrap values. So is there a way I can generate a Bewick file with both these values.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stamatak/standard-RAxML/issues/59#issuecomment-975131926, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGXB6TMK6MXYAXLK7HEPADUNHGKPANCNFSM5ILMC55Q. 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.

-- 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