MCMCTree without codon alignment

[Avehi Singh]

Hi,

I have generated a species tree topology for my group of interest using ASTRAL and am trying to time calibrate this topology using MCMCTree. ASTRAL uses gene trees as input and therefore I don't have a sequence alignment file for input to MCMCTree. Can I use this program without an alignment?

Thank you in advance!

Avehi

[Sandra AC]

Hi there,

MCMCtree requires two input files: the sequence file with the sequence alignment and the tree file with a fixed tree topology. Without these input files, you will not be able to run MCMCtree, unfortunately. Please find more details about the required input files and how to prepare the control file t run this program on the PAML documentation.

Hope this helps!
S.