Actually, what I want to do is that I am following a paper where they used Mesquite to generate their datasets for testing ancestral protein reconstruction. Specifically they generated "Random phylogenetic trees with 25,40,60,90,130,175,235,325,440 and 600 tips under the Yule Model, with unit scale and index of stability ranging from 1.0 to 2.0 in steps of 0.2" . This gave to the "raise of 60 experimental conditions, each consisting of 250 trees and simulated datasets, with variable tree size and index of stability of simulated trait values". The paper is 6 years old, so I a guessing some things have changed in the Mesquite suite, but if you could give some guidelines on how to reproduce their conditions I would be very very thankful. They do not specify which trees they used to make the simulations, so perhaps some of the examples that the Mesquite suite provides? I think that would be enough
Hi!
I am using Mesquite version 3.61
I would like to make some DNA simulations (which I think I managed to do by following http://mesquiteproject.org/mesquiteArchives/mesquite2.75/Mesquite_Folder/docs/mesquite/RandomSimul/simDNA.html) and obtain both the leaves and the internal/ancestors sequences. I have only the leaves sequences and in order to obtain the internal nodes, I am following the old manual (http://andrelevy.net/bioinfo/mesquite/Mesquite2Manual.pdf) mixed with the info at the website mesquiteproject.org.
According to this http://mesquiteproject.org/mesquiteArchives/mesquite2.75/Mesquite_Folder/docs/mesquite/RandomSimul/simChars.html, I would be able to generate the ancestral sequences by activating the Trace Character History under the Tree window in the Analysis tab. Well, that option is not there and neither I can find it (I have clicked everywhere). Is the website/manual outdated? I hope these options are still available somewhere...
Actually, what I want to do is that I am following a paper where they used Mesquite to generate their datasets for testing ancestral protein reconstruction. Specifically they generated "Random phylogenetic trees with 25,40,60,90,130,175,235,325,440 and 600 tips under the Yule Model, with unit scale and index of stability ranging from 1.0 to 2.0 in steps of 0.2" . This gave to the "raise of 60 experimental conditions, each consisting of 250 trees and simulated datasets, with variable tree size and index of stability of simulated trait values". The paper is 6 years old, so I a guessing some things have changed in the Mesquite suite, but if you could give some guidelines on how to reproduce their conditions I would be very very thankful. They do not specify which trees they used to make the simulations, so perhaps some of the examples that the Mesquite suite provides? I think that would be enough
Thanks for your time and help!!