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Updated: Oct 9, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR-JOINING
James S Farris1, Victor A Albert2, Mari Källersjö1
1Molekylärsystematiska laboratoriet, Naturhistoriska riksmuseet, Box 50007, Stockholm, S 104 05, Sweden.
Abstract:
Abstract- Because they are designed to produced just one tree, neighbor-joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor-joining programs may give misleading bootstrap frequencies because they do not suppress zero-length branches and/or are sensitive to the order of terminals in the data. A new procedure, parsimony jackknifing, overcomes these problems while running hundreds of times faster than existing programs for neighbor-joining bootstrapping. For analysis of large matrices, parsimony jackknifing is hundreds of thousands of times faster than extensive branch-swapping, yet is better able to screen out poorly-supported groups.
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