Abstract
This study assesses characteristics of the normalized compression distance (NCD) technique for building phylogenetic trees from molecular data. We examined results from a mammalian biological data set as well as a collection of simulated data with varying levels of incomplete lineage sorting. The implementation of NCD we analyze is a concatenation-based, distance-based, alignment-free, and model-free phylogeny estimation method, which takes concatenated unaligned sequence data as input and outputs a matrix of distances. We compare the NCD phylogeny estimation method with various other methods, including coalescent- and concatenation-based methods.
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