Greetings,
Is there a way to extract evolutionary lineages from phylogenetic trees? I am working on 465 bacterial sequences. The bacteria I am working with has known Lineage 1 and Lineage 2. I am examining the emergence of a newer lineage, which I will call 2.1. I do not know how many of the sequences belong to lineage 1 0r 2 or 2.1, but I have reference sequences and some known sequences for each of these lineages. I did RAxML analysis and I have the RAxML best tree file. I would like to extract Lineages from this. Looking at the tree looks confusing more so is attempting to extract manually. How can I extract these lineages? Any program? or anything I can use?
Cheers!
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edited you title, no need to shout ;-)
not sure how applicable for for your case: but you could have a look at tree reconciliation software ?
I believe this is possible in
dendropy, so you might want to take a look there if you're comfortable with python.