A new sequence distance measure for phylogenetic tree construction.
BACKGROUND
Most existing approaches for phylogenetic inference use multiple alignment of sequences and assume some sort of an evolutionary model. The multiple alignment strategy does not work for all types of data, e.g. whole genome phylogeny, and the evolutionary models may not always be correct. We propose a new sequence distance measure based on the relative information between the sequences using Lempel-Ziv complexity. The distance matrix thus obtained can be used to construct phylogenetic trees.


RESULTS
The proposed approach does not require sequence alignment and is totally automatic. The algorithm has successfully constructed consistent phylogenies for real and simulated data sets.


BACKGROUND
Available on request from the authors.
Department of Electrical Engineering, University of Nebraska-Lincoln, 209N WSEC, Lincoln, NE 68503, USA. hotu@bidmc.harvard.edu
Hasan H
HH
Otu
Khalid
K
Sayood
D000465:Algorithms; D000818:Animals; D002874:Chromosome Mapping / Q000379:methods*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008928:Mitochondria / Q000235:genetics*; D010802:Phylogeny; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity