2005/11/20 by Asger Hobolth, Ruriko Yoshida, Hobolth, Asger +1
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Evolution and Paleontology Studies #FOS: Biological sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Quantitative Methods (q-bio.QM) #q-bio.QM
paper · pdf · doi:10.48550/arxiv.q-bio/0511034
12 pages. To appear in Algebaic Biology 2005
arxiv created 2005/11/20 · openalex publication_date 2005/11/20 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
A central task in the study of molecular sequence data from present-day species is the reconstruction of the ancestral relationships. The most established approach to tree reconstruction is the maximum likelihood (ML) method. In this method, evolution is described in terms of a discrete-state continuous-time Markov process on a phylogenetic tree. The substitution rate matrix, that determines the Markov process, can be estimated using the expectation maximization (EM) algorithm. Unfortunately, an exhaustive search for the ML phylogenetic tree is computationally prohibitive for large data sets. In such situations, the neighbor-joining (NJ) method is frequently used because of its computational speed. The NJ method reconstructs trees by clustering neighboring sequences recursively, based on pairwise comparisons between the sequences. The NJ method can be generalized such that reconstruction is based on comparisons of subtrees rather than pairwise distances. In this paper, we present an algorithm for simultaneous substitution rate estimation and phylogenetic tree reconstruction. The algorithm iterates between the EM algorithm for estimating substitution rates and the generalized NJ method for tree reconstruction. Preliminary results of the approach are encouraging.