These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
22. 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. PubMed ID: 16412478 [TBL] [Abstract][Full Text] [Related]
23. Evolutionary tree reconstruction using structural expectation maximization and homotopy. Li J; Guo M Genet Mol Res; 2007 Sep; 6(3):522-33. PubMed ID: 17985305 [TBL] [Abstract][Full Text] [Related]
24. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Liu K; Raghavan S; Nelesen S; Linder CR; Warnow T Science; 2009 Jun; 324(5934):1561-4. PubMed ID: 19541996 [TBL] [Abstract][Full Text] [Related]
25. Random local neighbor joining: a new method for reconstructing phylogenetic trees. Zhang W; Sun Z Mol Phylogenet Evol; 2008 Apr; 47(1):117-28. PubMed ID: 18343690 [TBL] [Abstract][Full Text] [Related]
26. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Eckert AJ; Carstens BC Mol Phylogenet Evol; 2008 Dec; 49(3):832-42. PubMed ID: 18845264 [TBL] [Abstract][Full Text] [Related]
27. MultiPhyl: a high-throughput phylogenomics webserver using distributed computing. Keane TM; Naughton TJ; McInerney JO Nucleic Acids Res; 2007 Jul; 35(Web Server issue):W33-7. PubMed ID: 17553837 [TBL] [Abstract][Full Text] [Related]
28. SDM: a fast distance-based approach for (super) tree building in phylogenomics. Criscuolo A; Berry V; Douzery EJ; Gascuel O Syst Biol; 2006 Oct; 55(5):740-55. PubMed ID: 17060196 [TBL] [Abstract][Full Text] [Related]
29. 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. PubMed ID: 10958856 [TBL] [Abstract][Full Text] [Related]
30. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Sullivan J; Abdo Z; Joyce P; Swofford DL Mol Biol Evol; 2005 Jun; 22(6):1386-92. PubMed ID: 15758203 [TBL] [Abstract][Full Text] [Related]
31. Estimating species phylogenies using coalescence times among sequences. Liu L; Yu L; Pearl DK; Edwards SV Syst Biol; 2009 Oct; 58(5):468-77. PubMed ID: 20525601 [TBL] [Abstract][Full Text] [Related]
32. Reciprocal illumination in the gene content tree of life. Lienau EK; DeSalle R; Rosenfeld JA; Planet PJ Syst Biol; 2006 Jun; 55(3):441-53. PubMed ID: 16861208 [TBL] [Abstract][Full Text] [Related]
33. Towards building the tree of life: a simulation study for all angiosperm genera. Salamin N; Hodkinson TR; Savolainen Coates V Syst Biol; 2005 Apr; 54(2):183-96. PubMed ID: 16012091 [TBL] [Abstract][Full Text] [Related]
34. A likelihood look at the supermatrix-supertree controversy. Ren F; Tanaka H; Yang Z Gene; 2009 Jul; 441(1-2):119-25. PubMed ID: 18502054 [TBL] [Abstract][Full Text] [Related]
35. Identifying hybridization events in the presence of coalescence via model selection. Kubatko LS Syst Biol; 2009 Oct; 58(5):478-88. PubMed ID: 20525602 [TBL] [Abstract][Full Text] [Related]
36. Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies. Kumar S; Gadagkar SR J Mol Evol; 2000 Dec; 51(6):544-53. PubMed ID: 11116328 [TBL] [Abstract][Full Text] [Related]
37. Neighbor-joining uses the optimal weight for net divergence. Charleston MA; Hendy MD; Penny D Mol Phylogenet Evol; 1993 Mar; 2(1):6-12. PubMed ID: 8081548 [TBL] [Abstract][Full Text] [Related]
38. Bayesian phylogeny analysis via stochastic approximation Monte Carlo. Cheon S; Liang F Mol Phylogenet Evol; 2009 Nov; 53(2):394-403. PubMed ID: 19589389 [TBL] [Abstract][Full Text] [Related]
39. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: a model. Meng C; Kubatko LS Theor Popul Biol; 2009 Feb; 75(1):35-45. PubMed ID: 19038278 [TBL] [Abstract][Full Text] [Related]