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Items: 1 to 20 of 149

1.

A practical O(n log2 n) time algorithm for computing the triplet distance on binary trees.

Sand A, Brodal GS, Fagerberg R, Pedersen CN, Mailund T.

BMC Bioinformatics. 2013;14 Suppl 2:S18. doi: 10.1186/1471-2105-14-S2-S18. Epub 2013 Jan 21.

2.

Fast calculation of the quartet distance between trees of arbitrary degrees.

Christiansen C, Mailund T, Pedersen CN, Randers M, Stissing MS.

Algorithms Mol Biol. 2006 Sep 25;1:16.

3.

QDist--quartet distance between evolutionary trees.

Mailund T, Pedersen CN.

Bioinformatics. 2004 Jul 10;20(10):1636-7. Epub 2004 Feb 12.

4.

tqDist: a library for computing the quartet and triplet distances between binary or general trees.

Sand A, Holt MK, Johansen J, Brodal GS, Mailund T, Pedersen CN.

Bioinformatics. 2014 Jul 15;30(14):2079-80. doi: 10.1093/bioinformatics/btu157. Epub 2014 Mar 20.

5.

Algorithms for computing the triplet and quartet distances for binary and general trees.

Sand A, Holt MK, Johansen J, Fagerberg R, Brodal GS, Pedersen CN, Mailund T.

Biology (Basel). 2013 Sep 26;2(4):1189-209. doi: 10.3390/biology2041189.

6.

A polynomial-time algorithm computing lower and upper bounds of the rooted subtree prune and regraft distance.

Kannan L, Li H, Mushegian A.

J Comput Biol. 2011 May;18(5):743-57. doi: 10.1089/cmb.2010.0045. Epub 2010 Dec 18.

PMID:
21166560
7.

A sub-cubic time algorithm for computing the quartet distance between two general trees.

Nielsen J, Kristensen AK, Mailund T, Pedersen CN.

Algorithms Mol Biol. 2011 Jun 3;6:15. doi: 10.1186/1748-7188-6-15.

8.

A fast tool for minimum hybridization networks.

Chen ZZ, Wang L, Yamanaka S.

BMC Bioinformatics. 2012 Jul 2;13:155. doi: 10.1186/1471-2105-13-155.

9.

Fast computation of distance estimators.

Elias I, Lagergren J.

BMC Bioinformatics. 2007 Mar 13;8:89.

10.

SPR distance computation for unrooted trees.

Hickey G, Dehne F, Rau-Chaplin A, Blouin C.

Evol Bioinform Online. 2008 Feb 9;4:17-27.

11.

A practical method for exact computation of subtree prune and regraft distance.

Wu Y.

Bioinformatics. 2009 Jan 15;25(2):190-6. doi: 10.1093/bioinformatics/btn606. Epub 2008 Nov 19.

12.

Counting glycans revisited.

Böcker S, Wagner S.

J Math Biol. 2014 Oct;69(4):799-816. doi: 10.1007/s00285-013-0721-3. Epub 2013 Aug 23.

PMID:
23974240
13.

Fast local search for unrooted Robinson-Foulds supertrees.

Chaudhary R, Burleigh JG, Fernández-Baca D.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1004-13. doi: 10.1109/TCBB.2012.47.

PMID:
22431553
14.

A simple fixed parameter tractable algorithm for computing the hybridization number of two (not necessarily binary) trees.

Piovesan T, Kelk SM.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):18-25. doi: 10.1109/TCBB.2012.134.

PMID:
23702540
15.

Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles.

Yu Y, Warnow T, Nakhleh L.

J Comput Biol. 2011 Nov;18(11):1543-59. doi: 10.1089/cmb.2011.0174. Epub 2011 Oct 28.

16.

Quantifying hybridization in realistic time.

Collins J, Linz S, Semple C.

J Comput Biol. 2011 Oct;18(10):1305-18. doi: 10.1089/cmb.2009.0166. Epub 2011 Jan 6.

PMID:
21210735
17.

Fixed-parameter tractability of the maximum agreement supertree problem.

Guillemot S, Berry V.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Apr-Jun;7(2):342-53. doi: 10.1109/TCBB.2008.93.

PMID:
20431153
18.

Recrafting the neighbor-joining method.

Mailund T, Brodal GS, Fagerberg R, Pedersen CN, Phillips D.

BMC Bioinformatics. 2006 Jan 19;7:29.

19.

An efficient algorithm for approximating geodesic distances in tree space.

Battagliero S, Puglia G, Vicario S, Rubino F, Scioscia G, Leo P.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1196-207. doi: 10.1109/TCBB.2010.121.

PMID:
21116041
20.

Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios.

Lyubetsky VA, Rubanov LI, Rusin LY, Gorbunov KY.

Biol Direct. 2012 Dec 22;7:48. doi: 10.1186/1745-6150-7-48.

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