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Items: 1 to 20 of 91

1.
2.

A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures.

Fukagawa D, Tamura T, Takasu A, Tomita E, Akutsu T.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S13. doi: 10.1186/1471-2105-12-S1-S13.

3.

Designing an A* algorithm for calculating edit distance between rooted-unordered trees.

Horesh Y, Mehr R, Unger R.

J Comput Biol. 2006 Jul-Aug;13(6):1165-76.

PMID:
16901235
4.

Phylogenetic identification of lateral genetic transfer events.

Beiko RG, Hamilton N.

BMC Evol Biol. 2006 Feb 11;6:15.

5.

A metric for phylogenetic trees based on matching.

Lin Y, Rajan V, Moret BM.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):1014-22. doi: 10.1109/TCBB.2011.157.

PMID:
22184263
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.

Properties of consensus methods for inferring species trees from gene trees.

Degnan JH, DeGiorgio M, Bryant D, Rosenberg NA.

Syst Biol. 2009 Feb;58(1):35-54. doi: 10.1093/sysbio/syp008. Epub 2009 Jun 4.

8.

MASTtreedist: visualization of tree space based on maximum agreement subtree.

Huang H, Li Y.

J Comput Biol. 2013 Jan;20(1):42-9. doi: 10.1089/cmb.2012.0243.

PMID:
23294272
9.

Estimating species trees from unrooted gene trees.

Liu L, Yu L.

Syst Biol. 2011 Oct;60(5):661-7. doi: 10.1093/sysbio/syr027. Epub 2011 Mar 28.

PMID:
21447481
11.

IDXL: Species Tree Inference Using Internode Distance and Excess Gene Leaf Count.

Bhattacharyya S, Mukherjee J.

J Mol Evol. 2017 Aug;85(1-2):57-78. doi: 10.1007/s00239-017-9807-7. Epub 2017 Aug 23.

PMID:
28835989
12.

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.

PMID:
19019848
13.

Measuring inconsistency in phylogenetic trees.

Willson SJ.

J Theor Biol. 1998 Jan 7;190(1):15-36.

PMID:
9473388
14.

The tree-edit-distance, a measure for quantifying neuronal morphology.

Heumann H, Wittum G.

Neuroinformatics. 2009 Sep;7(3):179-90. doi: 10.1007/s12021-009-9051-4. Epub 2009 May 28.

PMID:
19475518
15.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
16.

Big cat phylogenies, consensus trees, and computational thinking.

Sul SJ, Williams TL.

J Comput Biol. 2011 Jul;18(7):895-906. doi: 10.1089/cmb.2010.0199. Epub 2011 May 12.

PMID:
21563975
17.

What is the danger of the anomaly zone for empirical phylogenetics?

Huang H, Knowles LL.

Syst Biol. 2009 Oct;58(5):527-36. doi: 10.1093/sysbio/syp047. Epub 2009 Aug 26.

PMID:
20525606
18.

ETE: a python Environment for Tree Exploration.

Huerta-Cepas J, Dopazo J, Gabaldón T.

BMC Bioinformatics. 2010 Jan 13;11:24. doi: 10.1186/1471-2105-11-24.

19.

Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design.

McCormack JE, Huang H, Knowles LL.

Syst Biol. 2009 Oct;58(5):501-8. doi: 10.1093/sysbio/syp045. Epub 2009 Aug 20.

PMID:
20525604
20.

Sequence alignment, mutual information, and dissimilarity measures for constructing phylogenies.

Penner O, Grassberger P, Paczuski M.

PLoS One. 2011 Jan 4;6(1):e14373. doi: 10.1371/journal.pone.0014373.

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