MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:
Dear MrBayes developers,
I'm experiencing the following issue:
I just run the two attached nexus. They are exactly the same, except the following difference: one of them is a single partition. The other one is one partition per site. The model is standard. I report the per site evolutionary rate.
As you will see, sites 2,3,4 are just missing data. I was expecting that the likelihood and eventually the rate of such sites will be just 1. However, this is not the case for the unpartitioned model. I'm sure that this is related somehow to the data participating in the calculation, but I cannot understand why both runs do not result in the same outcome. If I need to estimate the per site rate, which of the two (partitioned or upartitioned is more appropriate)?
single.log is associated with the [nex_sites_single.txt]
fixed.log is associated with [nex_sites_fixed.txt]
fixed.log
Dear MrBayes developers, I'm experiencing the following issue: I just run the two attached nexus. They are exactly the same, except the following difference: one of them is a single partition. The other one is one partition per site. The model is standard. I report the per site evolutionary rate.
As you will see, sites 2,3,4 are just missing data. I was expecting that the likelihood and eventually the rate of such sites will be just 1. However, this is not the case for the unpartitioned model. I'm sure that this is related somehow to the data participating in the calculation, but I cannot understand why both runs do not result in the same outcome. If I need to estimate the per site rate, which of the two (partitioned or upartitioned is more appropriate)?
single.log is associated with the [nex_sites_single.txt] fixed.log is associated with [nex_sites_fixed.txt] fixed.log
I also attach the log files single.log part.log
best pavlos
nex_sites_fixed.txt nex_sites_single.txt
What is the current observed behaviour?
What is the expected/wanted behaviour?
How may we reproduce this bug?
Steps to reproduce the bug: 1. 2. 3. 4.
Would you be able to compile and run MrBayes to test fixes to this bug?
gitand how to compile MrBayes.What is the environment that you run MrBayes in?
Versioncommand in MrBayes below:Other information that may be of use to us in resolving this issue