phylogenetic reconstruction to detect loss - Githubissues

jasminelmah / finalproject

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phylogenetic reconstruction to detect loss #8

Open caseywdunn opened 5 years ago

caseywdunn commented 5 years ago

You could identify candidates for loss as follows:

For each homolog:

Identify all the tips in which the homolog is present
Identify the node number of the most recent common ancestor MRCA of this species
Create a vector with one element per homolog and the value is the MRCA

candidates for loss:

A gene that is absent in a tip but present in the ancestor of the tip