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Items: 1 to 20 of 193

1.

LNETWORK: an efficient and effective method for constructing phylogenetic networks.

Wang J, Guo M, Liu X, Liu Y, Wang C, Xing L, Che K.

Bioinformatics. 2013 Sep 15;29(18):2269-76. doi: 10.1093/bioinformatics/btt378. Epub 2013 Jun 29.

PMID:
23811095
2.

BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.

Wang J, Guo M, Xing L, Che K, Liu X, Wang C.

Gene. 2013 Sep 15;527(1):344-51. doi: 10.1016/j.gene.2013.06.036. Epub 2013 Jun 28.

PMID:
23816409
3.

Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters.

van Iersel L, Kelk S, Rupp R, Huson D.

Bioinformatics. 2010 Jun 15;26(12):i124-31. doi: 10.1093/bioinformatics/btq202.

4.

A Survey of Methods for Constructing Rooted Phylogenetic Networks.

Wang J.

PLoS One. 2016 Nov 2;11(11):e0165834. doi: 10.1371/journal.pone.0165834. eCollection 2016.

5.

A new algorithm to construct phylogenetic networks from trees.

Wang J.

Genet Mol Res. 2014 Mar 6;13(1):1456-64. doi: 10.4238/2014.March.6.4.

6.

HybridNET: a tool for constructing hybridization networks.

Chen ZZ, Wang L.

Bioinformatics. 2010 Nov 15;26(22):2912-3. doi: 10.1093/bioinformatics/btq548. Epub 2010 Sep 24.

PMID:
20871109
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.

How much information is needed to infer reticulate evolutionary histories?

Huber KT, Van Iersel L, Moulton V, Wu T.

Syst Biol. 2015 Jan;64(1):102-11. doi: 10.1093/sysbio/syu076. Epub 2014 Sep 18.

9.

Constructing Phylogenetic Networks Based on the Isomorphism of Datasets.

Wang J, Zhang Z, Li Y.

Biomed Res Int. 2016;2016:4236858. doi: 10.1155/2016/4236858. Epub 2016 Jul 28.

10.

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
11.

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.

Chaudhary R, Fernández-Baca D, Burleigh JG.

Bioinformatics. 2015 Feb 1;31(3):432-3. doi: 10.1093/bioinformatics/btu648. Epub 2014 Oct 1.

PMID:
25273112
12.

On the elusiveness of clusters.

Kelk SM, Scornavacca C, van Iersel L.

IEEE/ACM Trans Comput Biol Bioinform. 2012;9(2):517-34. doi: 10.1109/TCBB.2011.128. Epub 2011 Sep 27.

PMID:
21968961
13.

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships.

Than C, Ruths D, Nakhleh L.

BMC Bioinformatics. 2008 Jul 28;9:322. doi: 10.1186/1471-2105-9-322.

14.

Application of phylogenetic networks in evolutionary studies.

Huson DH, Bryant D.

Mol Biol Evol. 2006 Feb;23(2):254-67. Epub 2005 Oct 12.

PMID:
16221896
15.

STEM: species tree estimation using maximum likelihood for gene trees under coalescence.

Kubatko LS, Carstens BC, Knowles LL.

Bioinformatics. 2009 Apr 1;25(7):971-3. doi: 10.1093/bioinformatics/btp079. Epub 2009 Feb 10.

PMID:
19211573
16.

An algorithm for constructing parsimonious hybridization networks with multiple phylogenetic trees.

Wu Y.

J Comput Biol. 2013 Oct;20(10):792-804. doi: 10.1089/cmb.2013.0072.

17.

Computing galled networks from real data.

Huson DH, Rupp R, Berry V, Gambette P, Paul C.

Bioinformatics. 2009 Jun 15;25(12):i85-93. doi: 10.1093/bioinformatics/btp217.

18.

Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks.

Van Iersel L, Kelk S, Mnich M.

J Bioinform Comput Biol. 2009 Aug;7(4):597-623.

PMID:
19634194
19.

Quartet-net: a quartet-based method to reconstruct phylogenetic networks.

Yang J, Grünewald S, Wan XF.

Mol Biol Evol. 2013 May;30(5):1206-17. doi: 10.1093/molbev/mst040. Epub 2013 Mar 14.

20.

Inferring phylogenetic relationships avoiding forbidden rooted triplets.

He YJ, Huynh TN, Jansson J, Sung WK.

J Bioinform Comput Biol. 2006 Feb;4(1):59-74.

PMID:
16568542

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