I am working in evolutionary biology of a family of proteins in plants, Human and Yeast and likewise have few query for the experts as follows
Is good idea to modify the phylogenetic tree as per our own requirements as some members are not clustered together from the same family. If Yes, please recommend me some free software for the same and If No, then what could be the possible explanation of such study for the publication. How to explain the fact that some gene families are not close to each other or overlapped with the different gene family. I tried some software but couldn't able to obtain it as per my wish.
Any suggestion will be appreciable
Thank you in advance