What’s the Answer? (modify a phylogenetic tree)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s question is something that was worth looking at if you are a phylogenetic tree novice. Not so much for the question itself, but for the gentle responses to a potentially questionable idea about altering a tree. I thought the responses were helpful guidance.

Question: How to edit Phylogenetic Trees as per required output and what are the softwares available to do the same


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


Be careful what you ask for…it may not be what you need. It’s possible that there are reasons to do some editing, but with bioinformatics tools there is a risk that such editing is not based on the real features but with an aim of making you data look the way you’d prefer. And that’s not what you ought to be doing. Check out the gentle admonishments in the answers.