Question: Extracting lineages from phylogenetic trees
gravatar for Fid_o
11 weeks ago by
Fid_o20 wrote:


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?


ADD COMMENTlink modified 6 weeks ago by Biostar ♦♦ 20 • written 11 weeks ago by Fid_o20

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 ?

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by lieven.sterck8.0k

I believe this is possible in dendropy, so you might want to take a look there if you're comfortable with python.

ADD REPLYlink written 11 weeks ago by Joe17k
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