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?
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Michael Kuhn
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.
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!
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