Question: Estimating Size Of Protein Families During Evolution
6
gravatar for Michael Kuhn
7.8 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

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?

evolution • 1.6k views
ADD COMMENTlink written 7.8 years ago by Michael Kuhn5.0k
3
gravatar for 14134125465346445
7.8 years ago by
United Kingdom
141341254653464453.5k wrote:

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.

ADD COMMENTlink written 7.8 years ago by 141341254653464453.5k

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!

ADD REPLYlink written 7.8 years ago by Michael Kuhn5.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 845 users visited in the last hour