How To Deal With The Sequence Divergence?
I have done the sequence alignment task of nearly 550 sequences of bacterial species by using Seaview program but while creating a phylogenetic tree from the same software it says that the sequences are too divergence. "Are they aligned?" Yes, I already did the alignment though. I don't want to reduce the number of sequences (I want to have the exhaustive search) to create a phylogenetic tree. Could some one please let me know how to deal with those sequence to create phylogenetic tree. I am using SeaView program for doing these tasks. Thanks lot in advance!
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spandankeshav •
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I am not sure but this discussion could be useful for
http://www.researchgate.net/post/What_software_works_in_constructing_phylogenetic_trees_from_thousands_of_sequences
I believe that you have to look out for some other program like RAxML which is good for large number of sequences.
Given that SeaView provides access to a selection of methods for generating a phylogenetic tree, which of the methods supported by SeaView have you tried and what did each one say?
If the methods are saying that the sequences in the alignment are too divergent, it suggests that the alignment may not contain any regions where all the sequences overlap. Check the alignment for fragments or unrelated sequences which could be causing problems.
I agree with Hamish. There could be no 'core' regions of genomic DNA that are present in all 550 sequences, so it can not build a tree. You may need to align in protein space or choose a subset of protein coding genes to use.