PhyD*: Fast NJ-like algorithms to deal with incomplete distance matrices.
Criscuolo A., Gascuel O.
BMC Bioinformatics. 2008, Mar 26;9:166.
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THIS paper if you use PhyD*.
Paper
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Gascuel O.
"Mathematical Hierarchies and Biology", Mirkin B., McMorris F.R., Roberts F.S., and Rzhetsky A. (Eds.).
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"The neighbor-joining method: a new method for reconstructing phylogenetic trees."
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