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Items: 1 to 20 of 94

1.

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.

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.

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.

4.

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.

5.

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.

PMID:
24651968
6.

QDist--quartet distance between evolutionary trees.

Mailund T, Pedersen CN.

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

PMID:
14962942
7.

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.

8.

Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction.

Sayyari E, Mirarab S.

BMC Genomics. 2016 Nov 11;17(Suppl 10):783. doi: 10.1186/s12864-016-3098-z.

9.

Extracting conflict-free information from multi-labeled trees.

Deepak A, Fernández-Baca D, McMahon MM.

Algorithms Mol Biol. 2013 Jul 9;8(1):18. doi: 10.1186/1748-7188-8-18.

10.

Towards sub-quadratic time and space complexity solutions for the dated tree reconciliation problem.

Drinkwater B, Charleston MA.

Algorithms Mol Biol. 2016 May 21;11:15. doi: 10.1186/s13015-016-0077-5. eCollection 2016.

11.

Quartet-based phylogenetic inference: improvements and limits.

Ranwez V, Gascuel O.

Mol Biol Evol. 2001 Jun;18(6):1103-16.

PMID:
11371598
12.

Quartet MaxCut: a fast algorithm for amalgamating quartet trees.

Snir S, Rao S.

Mol Phylogenet Evol. 2012 Jan;62(1):1-8. doi: 10.1016/j.ympev.2011.06.021. Epub 2011 Jul 6.

PMID:
21762785
13.

SPR distance computation for unrooted trees.

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

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

14.

Optimal algorithms for local vertex quartet cleaning.

Della Vedova G, Wareham HT.

Bioinformatics. 2002 Oct;18(10):1297-304.

PMID:
12376373
15.

Fast computation of distance estimators.

Elias I, Lagergren J.

BMC Bioinformatics. 2007 Mar 13;8:89.

16.
17.

Computing the all-pairs quartet distance on a set of evolutionary trees.

Stissing M, Mailund T, Pedersen CN, Brodal GS, Fagerberg R.

J Bioinform Comput Biol. 2008 Feb;6(1):37-50.

PMID:
18324744
18.

On the fixed parameter tractability of agreement-based phylogenetic distances.

Bordewich M, Scornavacca C, Tokac N, Weller M.

J Math Biol. 2017 Jan;74(1-2):239-257. doi: 10.1007/s00285-016-1023-3. Epub 2016 May 25.

PMID:
27221239
19.

An efficient algorithm for testing the compatibility of phylogenies with nested taxa.

Deng Y, Fernández-Baca D.

Algorithms Mol Biol. 2017 Mar 16;12:7. doi: 10.1186/s13015-017-0099-7. eCollection 2017.

20.

Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees.

Huson D, Linz S.

IEEE/ACM Trans Comput Biol Bioinform. 2016 Mar 2. [Epub ahead of print]

PMID:
26955052

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