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On the optimality of the neighbor-joining algorithm.

Eickmeyer K, Huggins P, Pachter L, Yoshida R.

Algorithms Mol Biol. 2008 Apr 30;3:5.PMID: 18447942 [PubMed]Related articlesFree article

Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle.

Desper R, Gascuel O.

J Comput Biol. 2002;9(5):687-705.PMID: 12487758 [PubMed - indexed for MEDLINE]Related articles

A multi-neighbor-joining approach for phylogenetic tree reconstruction and visualization.

Silva AE, Villanueva WJ, Knidel H, Bonato VC, Reis SF, Von Zuben FJ.

Genet Mol Res. 2005 Sep 30;4(3):525-34.PMID: 16342037 [PubMed - indexed for MEDLINE]Related articlesFree article

A rapid heuristic algorithm for finding minimum evolution trees.

Rodin A, Li WH.

Mol Phylogenet Evol. 2000 Aug;16(2):173-9.PMID: 10942605 [PubMed - indexed for MEDLINE]Related articles

A signal-to-noise analysis of phylogeny estimation by neighbor-joining: Insufficiency of polynomial length sequences.

Lacey MR, Chang JT.

Math Biosci. 2006 Feb;199(2):188-215. Epub 2006 Jan 18.PMID: 16412478 [PubMed - indexed for MEDLINE]Related articles

Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference.

Bordewich M, Gascuel O, Huber KT, Moulton V.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jan-Mar;6(1):110-7.PMID: 19179704 [PubMed - indexed for MEDLINE]Related articles

NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods.

Ota S, Li WH.

Mol Biol Evol. 2000 Sep;17(9):1401-9.PMID: 10958856 [PubMed - indexed for MEDLINE]Related articlesFree article

An approach of orthology detection from homologous sequences under minimum evolution.

Kim KM, Sung S, Caetano-Anollés G, Han JY, Kim H.

Nucleic Acids Res. 2008 Oct;36(17):e110. Epub 2008 Aug 1.PMID: 18676448 [PubMed - indexed for MEDLINE]Related articlesFree article

Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method.

Evans J, Sheneman L, Foster J.

J Mol Evol. 2006 Jun;62(6):785-92. Epub 2006 Apr 28.PMID: 16752216 [PubMed - indexed for MEDLINE]Related articles

Neighbor joining algorithms for inferring phylogenies via LCA distances.

Gronau I, Moran S.

J Comput Biol. 2007 Jan-Feb;14(1):1-15.PMID: 17381342 [PubMed - indexed for MEDLINE]Related articles

A stepwise algorithm for finding minimum evolution trees.

Kumar S.

Mol Biol Evol. 1996 Apr;13(4):584-93.PMID: 8882501 [PubMed - indexed for MEDLINE]Related articlesFree article

Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting.

Desper R, Gascuel O.

Mol Biol Evol. 2004 Mar;21(3):587-98. Epub 2003 Dec 23.PMID: 14694080 [PubMed - indexed for MEDLINE]Related articlesFree article

Combinatorics of least-squares trees.

Mihaescu R, Pachter L.

Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13206-11. Epub 2008 Sep 8.PMID: 18779558 [PubMed - indexed for MEDLINE]Related articlesFree article

Clearcut: a fast implementation of relaxed neighbor joining.

Sheneman L, Evans J, Foster JA.

Bioinformatics. 2006 Nov 15;22(22):2823-4. Epub 2006 Sep 18.PMID: 16982706 [PubMed - indexed for MEDLINE]Related articlesFree article

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

Gascuel O.

Mol Biol Evol. 1997 Jul;14(7):685-95.PMID: 9254330 [PubMed - indexed for MEDLINE]Related articlesFree article

Minimum evolution using ordinary least-squares is less robust than neighbor-joining.

Willson SJ.

Bull Math Biol. 2005 Mar;67(2):261-79.PMID: 15710181 [PubMed - indexed for MEDLINE]Related articles

Random local neighbor joining: a new method for reconstructing phylogenetic trees.

Zhang W, Sun Z.

Mol Phylogenet Evol. 2008 Apr;47(1):117-28. Epub 2008 Feb 1.PMID: 18343690 [PubMed - indexed for MEDLINE]Related articles

Comparison of additive trees using circular orders.

Makarenkov V, Leclerc B.

J Comput Biol. 2000;7(5):731-44.PMID: 11153096 [PubMed - indexed for MEDLINE]Related articles

Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates.

Levy D, Yoshida R, Pachter L.

Mol Biol Evol. 2006 Mar;23(3):491-8. Epub 2005 Nov 9.PMID: 16280538 [PubMed - indexed for MEDLINE]Related articlesFree article

A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joining.

Guo MZ, Li JF, Liu Y.

BMC Bioinformatics. 2008 May 28;9 Suppl 6:S4.PMID: 18541057 [PubMed - indexed for MEDLINE]Related articlesFree article