Publications

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2012
J. Wang, Guo, M. - Z., and Xing, L. L., FastJoin, an improved neighbor-joining algorithm, vol. 11. pp. 1909-1922, 2012.
Elias I and Lagergren J (2005). Fast Neighbor Joining. In: Proceedings of the 32nd International Colloquium: 11-15 July 2005 (L Caires, GF Italiano, L Monteiro, C Palamidessi, et al., eds.). Springer Berlin Heidelberg, Lisbon, 1263-1274.   Elias I and Lagergren J (2009). Fast neighbor joining. Theor. Comput. 410: 1993-2000. http://dx.doi.org/10.1016/j.tcs.2008.12.040   Evans J, Sheneman L and Foster J (2006). Relaxed neighbor joining: a fast distance-based phylogenetic tree construction method. J. Mol. Evol. 62: 785-792. http://dx.doi.org/10.1007/s00239-005-0176-2 PMid:16752216   Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, et al. (2006). Pfam: clans, web tools and services. Nucleic Acids Res. 34: D247-D251. http://dx.doi.org/10.1093/nar/gkj149 PMid:16381856 PMCid:1347511   Howe K, Bateman A and Durbin R (2002). QuickTree: building huge neighbor-joining trees of protein sequences. Bioinformatics 18: 1546-1547. http://dx.doi.org/10.1093/bioinformatics/18.11.1546 PMid:12424131   Mailund T and Pedersen CNS (2004). QuickJoin - fast neighbor-joining tree reconstruction. Bioinformatics 20: 3261- 3262. http://dx.doi.org/10.1093/bioinformatics/bth359 PMid:15201185   Mailund T, Brodal GS, Fagerberg R, Pedersen CNS, et al. (2006). Recrafting the neighbor-joining method. BMC Bioinformatics 7: 29. http://dx.doi.org/10.1186/1471-2105-7-29 PMid:16423304 PMCid:3271233   Nakhleh L, Moret BME, Roshan U and John KS (2002). The Accuracy of Fast Phylogenetic Methods for Large Datasets. In: Proceedings of the Seventh Pacific Symposium on Biocomputing: 2001 (Altman RB, Dunker AK, Hunter L, Lauderdale K, et al., eds.). World Scientific, Singapore, 211-222. PMid:11928477   Price MN, Dehal PS and Arkin AP (2009). FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26: 1641-1650. http://dx.doi.org/10.1093/molbev/msp077 PMid:19377059 PMCid:2693737   Price MN, Dehal PS and Arkin AP (2010). FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490. http://dx.doi.org/10.1371/journal.pone.0009490 PMid:20224823 PMCid:2835736   Saitou N and Nei M (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. PMid:3447015   Sheneman L, Evans J and Foster JA (2006). Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22: 2823-2824. http://dx.doi.org/10.1093/bioinformatics/btl478 PMid:16982706   Simonsen M, Mailund T and Pedersen CNS (2008). Rapid Neighbor-Joining. In: Proceedings of the Eighth International Workshop on Algorithms in Bioinformatics: 15-19 September 2008 (Crandall KA and Lagergren J, eds.). Springer Berlin Heidelberg, Karlsruhe, 113-122. http://dx.doi.org/10.1007/978-3-540-87361-7_10   Simonsen M, Mailund T and Pedersen CNS (2011). Inference of Large Phylogenies Using Neighbor-Joining. In: Proceedings of the Third International Joint Conference: 20-23 January 2010 (Fred A, Filipe J and Gamboa H, eds.). Springer Berlin Heidelberg, Valencia, 334-344. PMCid:3224425   Studier JA and Keppler KJ (1988). A note on the neighbor-joining algorithm of Saitou and Nei. Mol. Biol. Evol. 5: 729- 731. PMid:3221794   Wheeler TJ (2009). Large-Scale Neighbor-Joining with NINJA. In: Proceedings of the Ninth International Workshop on Algorithms in Bioinformatics: 12-13 September 2009 (Salzberg SL and Warnow T, eds.). Springer Berlin Heidelberg, Philadelphia, 375-389.   Zaslavsky L and Tatusova T (2008). Accelerating the Neighbor-Joining Algorithm Using the Adaptive Bucket Data Structure. In: Proceedings of the Fourth International Symposium: 6-9 May 2008 (Mandoiu I, Sunderraman R and Zelikovsky A, eds.). Springer Berlin Heidelberg, Atlanta, 122-133.