Ana Estela A. da Silva, Wilfredo J.P. Villanueva, Helder Knidel, Vinícius Bonato, Sérgio F. dos Reis, Fernando J. Von Zuben
Published September 30, 2005
Genet. Mol. Res. 4 (3): 525-534 (2005)

About the Authors
Ana Estela A. da Silva, Wilfredo J.P. Villanueva, Helder Knidel, Vinícius Bonato, Sérgio F. dos Reis, Fernando J. Von Zuben

Corresponding author
W.J.P. Villanueva
Email: wilfredo@dca.fee.unicamp.br

ABSTRACT

The computationally challenging problem of reconstructing the phylogeny of a set of contemporary data, such as DNA sequences or morphological attributes, was treated by an extended version of the neighbor-joining (NJ) algorithm. The original NJ algorithm provides a single-tree topology, after a cascade of greedy pairing decisions that tries to simultaneously optimize the minimum evolution and the least squares criteria. Given that some sub-trees are more stable than others, and that the minimum evolution tree may not be achieved by the original NJ algorithm, we propose a multi-neighbor-joining (MNJ) algorithm capable of performing multiple pairing decisions at each level of the tree reconstruction, keeping various partial solutions along the recursive execution of the NJ algorithm. The main advantages of the new recstruction procedure are: 1) as is the case for the original NJ algorithm, the MNJ algorithm is still a low-cost reconstruction method; 2) a further investigation of the alternative topologies may reveal stable and unstable sub-trees; 3) the chance of achieving the minimum evolution tree is greater; 4) tree topologies with very similar performances will be simultaneously presented at the output. When there are multiple unrooted tree topologies to be compared, a visualization tool is also proposed, using a radial layout to uniformly distribute the branches with the help of well-known metaheuristics used in computer science.

Key words: Fitch-Margoliash method, Multi-neighbor-joining algorithm, Unrooted tree visualization, Phylogenetic tree reconstruction.