Analysis of Gene Tree
I am reconstructing a gene tree of geneA of a bacterial strain. Some sequences were identical. Should I include those sequences in Tree analysis. If yes then what posible explanation for that.
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h.mon
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amreshsharma.100 •
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amreshsharma.100 •
1 answer
Two interesting posts:
How do exactly identical sequences in the alignment effect the log(likelihood) score?
Phylogenetic tree editing: Reinserting removed identical sequences
I will quote the response by Alexandros Stamatakis (RAxML author) from the first link, so my answer consists of more than just links:
That's a good way to do it, I'd remove the duplicate seqs though because
they don't provide additional info
the analyses will run faster with less seqs
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Yes, you have to include them. Those bacteria are very close
relatives and/or this is an important gene, some mutations spoil its
function and evolution got rid of such bacteria (with mutated gene).
What do you think the explanation is?