Estimating Size Of Protein Families During Evolution

Question

[Michael Kuhn]

I would like to simply estimate gene duplication / loss for multiple protein families, given both a phylogenetic tree and the number of copies for different species.

For example:

Human: 3   ---\________
Chimp: 3   ---/        \_______
Mouse: 2   ---\__      /
Rat:   1   ---/  \____/
Guinea pig: 2 ---/

Should output: 2 proteins in the common ancestor, 1 loss for rat, duplication for apes. My real phylogenetic tree doesn't have branch lengths, and has multifurcations. Is there a simple tool to reconstruct the history of such a protein family?

Answer 1

[14134125465346445]

You can use something like Christian Zmasek's tool published 11 years ago: http://bioinformatics.oxfordjournals.org/content/17/9/821.short

There are other tools out there that are similar to it and came after this one.

[Michael Kuhn]

Thanks! The link in the paper is broken, unsurprisingly after 11 years, but there's a new site: http://www.phylosoft.org/forester/applications/sdi/ – I'll check it out!