Which program can analyze character evolution

Question

[Yongjie Zhang]

Hello All,

In my fungus, I found diverse intron presence/absence dynamics among different isolates. I have built a tree using exon sequences and want to infer what evolutionary events ever occurred for introns based on the exon tree. That is, how many times of intron loss and how many times of intron gain events were there in the evolutionary history?

I know MacClade should help me, but MacClade never works in newer versions of Mac computers. Do you know any other programs that I can use and that is easy to learn?

Thanks

Yongjie

[Yongjie Zhang]

Thanks for your reply, David.

Actually, I've performed ancestral state construction using the RASP program. I know Mesquite but never used it. I'm not sure whether the R functions you mentioned are able to infer the numbers of intron gain/loss events. I'm looking for a tool that can accept a phylogenetic tree and the intron presence/absence data as inputs.

[David W]

Hi Yongjie, I moved your post to a comment, as the answer section should really be reserved to answers to the question in the top post.

In answer to your follow-up, any of those methods with take a tree and corresponding presence-absence data as inputs. The simmap function in phytools is specifically for inferring the number of changes of character state while taking uncertainty and reversion into account.

Answer 1

[David W]

There are a huge number of tools for studying character evolution in a phylogenetic framework.

You mention MacClade, which was more or less trimmed down version of Mesquite. If you are comfortable with MacClade you can probably adapt to Mesquite. Alternatively, there are packages in R that do ancestral state construction, including the functions 'ace' in the package 'ape' and 'make.simmap' in phytools.