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Some minor question regarding the output of mcmctree when using usedata = 3

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­임원섭 / 학생 / 지구과학교육과

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Nov 18, 2024, 10:19:32 AM11/18/24
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Hi, 

I'm trying to estimate divergence time using genome-scale amino acid alignment with mcmctree. I'm following the tutorial (http://abacus.gene.ucl.ac.uk/software/MCMCtree.Tutorials.pdf) and it states to obtain the Hessian matrix for the protein substitution model (other than the basic Poisson model), I have to run mcmctree with the usedata=3 option, then delete out.BV and rst files before running codeml to obtain the final matrix. However, when I ran mcmctree with usedata=3 multiple rst files (rst, rst1, rst2) were generated. 
What are the differences between these rst files? Should I delete all rst (including rst1 and rst2) files before running codeml or just "rst"? 

Thanks in advance!

Sishuo Wang

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Nov 19, 2024, 1:41:39 AM11/19/24
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Dear David,

you are almost there. rst2 should be used, if you open that file, you will see it contains the branch length MLEs, gradient, and hessian of the log-likelihood evaluated at the MLEs, which are perfectly enough to perform the approximate likelihood dating by mcmctree "usedata=2" later.

best,
sishuo

­임원섭 / 학생 / 지구과학교육과

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Nov 19, 2024, 2:17:10 AM11/19/24
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Dear Dr. Wang. 

Thank you for the reply. 
So, does this mean that I don't have to care about rst files (rst, rst1, rst2) generated from the usedata=3 run and rst and rst1 files from the codml run?

2024년 11월 19일 화요일 오후 3시 41분 39초 UTC+9에 Sishuo Wang님이 작성:

Sishuo Wang

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Nov 20, 2024, 9:31:40 PM11/20/24
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Dear David,

I think either out.BV or rst2 works, they should have exactly the same content. Then follow the tutorial, rename out.BV to in.BV, and set usedata=2 in.BV 1, the last number representing the way of branch length value transform (see dos reis & yang 2011) [but this may not be very important]. Should further Qs, pls don't hesitate to post your Qs here. thanks!

best,
sishuo

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