I have constructed phylogenetic trees for my data set using three different approaches, namely MP, ML, and BI. When I submited the paper, one reviewer commented our phylogenetic approaches below.
I still do not really understand why MP is used to reconstruct phylogenetic trees, because BI and ML are used as well. It is of course a matter of choice, but if MP is used with molecular data, molecular evolution should be implemented as well as possible in the analysis, e.g. via adjusted Ti/Tv, step matrices, ... ideally not using ML to define the values used, else just use ML to make the tree if the analysis is feasible, as it is the case here
In my analysis with MP, I had gaps treated as the fifth base, so it's not allowed to set Ti/Tv step matrices because of conflicts of the two settings. Can you tell what phylogenetic approaches you generally use? Also, can you suggest how to respond this comment? Thanks.