Neighbour Joining Software For Very Large Dataset
I have a friend that need to generate a NJ tree for a dataset containing ~84000 species. What would be the best solution?
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Adam Monier •
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Paulo Nuin
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Paulo Nuin
2 answers
For large datasets try "composition vector method" + NJ tree.
CV/NJ approach is fairly consistent with the trees generated by traditional approaches.
For faster alignments try MUSCLE instead of clustalw.
Rapid DNA barcoding analysis of large datasets using the composition vector method
I would personally drop the NJ approach and go for an approximately-maximum-likelihood phylogenetic reconstruction using the (extremely) fast and reliable tool FastTree.
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