Analysis of Gene Tree

Question

[amreshsharma.100]

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.

[natasha.sernova]

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).

[Joe]

What do you think the explanation is?

Answer 1

[h.mon]

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

1. they don't provide additional info

2. the analyses will run faster with less seqs