I am currently doing a phylogenetic analysis for a species of virus having many subtypes (Human papillomavirus) for around 100 whole genome specimen and 50 partial sequences belonging to ~6 subtypes. Is there a specific number of Maximum Likelihood / Bayesian Inference trees I need to infer for the phylogenetic study to be accurate?
At the moment for ML I aligned the sequences with ClustalO and
using RAxML with 25 ML trees and autoMRE stopping criterion. But I have no idea if 25ML treees is enough for the analysis
That depends on which parts of the tree you want accuracy in. Surely all of the trees will have all of the viruses assigned to the right subtype. The differences will be trivial differences in branching order within a given subtype.
Hi Manuel,
Concerning Bayesian analyses there are some parameters that can be checked to see if the analyses have been run for enough time. You can check the “average standard deviation of split frequencies” (if you run MrBayes for example). You can check it in the program screen log while the analyses are running. Usually values below 0.01 are considered acceptable.
Which program are you using?
Alternatively, you can check the output files in Tracer. If you have values of ESS above 200 for the different parameters, the analyses are ok.
I hope it helps,
Salvatore
- Badges
- Science method
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics
- Phylogenetic Analysis