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Items: 1 to 20 of 120

1.

COPYCAT: cophylogenetic analysis tool.

Meier-Kolthoff JP, Auch AF, Huson DH, Göker M.

Bioinformatics. 2007 Apr 1;23(7):898-900. Epub 2007 Jan 31.

PMID:
17267434
2.

Traversing the tangle: algorithms and applications for cophylogenetic studies.

Charleston MA, Perkins SL.

J Biomed Inform. 2006 Feb;39(1):62-71. Epub 2005 Sep 26. Review.

3.

A congruence index for testing topological similarity between trees.

de Vienne DM, Giraud T, Martin OC.

Bioinformatics. 2007 Dec 1;23(23):3119-24. Epub 2007 Oct 12.

PMID:
17933852
4.

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization.

Blum T, Kohlbacher O.

Bioinformatics. 2008 Sep 15;24(18):2108-9. doi: 10.1093/bioinformatics/btn360. Epub 2008 Jul 16.

5.

HyPhy: hypothesis testing using phylogenies.

Pond SL, Frost SD, Muse SV.

Bioinformatics. 2005 Mar 1;21(5):676-9. Epub 2004 Oct 27.

PMID:
15509596
6.

Cophylogenetic Reconciliation with ILP.

Wieseke N, Hartmann T, Bernt M, Middendorf M.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Nov-Dec;12(6):1227-35. doi: 10.1109/TCBB.2015.2430336.

PMID:
26671795
7.

CTree: comparison of clusters between phylogenetic trees made easy.

Archer J, Robertson DL.

Bioinformatics. 2007 Nov 1;23(21):2952-3. Epub 2007 Aug 23.

PMID:
17717036
8.

Phylogenetic trees based on gene content.

Huson DH, Steel M.

Bioinformatics. 2004 Sep 1;20(13):2044-9. Epub 2004 Mar 25.

PMID:
15044248
9.

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.

Friedrich J, Dandekar T, Wolf M, Müller T.

Bioinformatics. 2005 May 1;21(9):2108-9. Epub 2005 Jan 27.

PMID:
15677706
10.

JCell--a Java-based framework for inferring regulatory networks from time series data.

Spieth C, Supper J, Streichert F, Speer N, Zell A.

Bioinformatics. 2006 Aug 15;22(16):2051-2. Epub 2006 Jun 16.

PMID:
16782725
11.
12.

A novel algorithm and web-based tool for comparing two alternative phylogenetic trees.

Nye TM, Liò P, Gilks WR.

Bioinformatics. 2006 Jan 1;22(1):117-9. Epub 2005 Oct 18.

PMID:
16234319
13.

When can host shifts produce congruent host and parasite phylogenies? A simulation approach.

de Vienne DM, Giraud T, Shykoff JA.

J Evol Biol. 2007 Jul;20(4):1428-38.

14.

Treevolution: visual analysis of phylogenetic trees.

Santamaría R, Therón R.

Bioinformatics. 2009 Aug 1;25(15):1970-1. doi: 10.1093/bioinformatics/btp333. Epub 2009 May 26.

PMID:
19470585
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.

PACo: a novel procrustes application to cophylogenetic analysis.

Balbuena JA, Míguez-Lozano R, Blasco-Costa I.

PLoS One. 2013 Apr 8;8(4):e61048. doi: 10.1371/journal.pone.0061048. Print 2013.

17.

AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa.

Stamatakis A, Auch AF, Meier-Kolthoff J, Göker M.

BMC Bioinformatics. 2007 Oct 22;8:405.

18.

Computational aspects of host-parasite phylogenies.

Stevens J.

Brief Bioinform. 2004 Dec;5(4):339-49. Review.

PMID:
15606970
19.

Dendroscope: An interactive viewer for large phylogenetic trees.

Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R.

BMC Bioinformatics. 2007 Nov 22;8:460.

20.

ModuleMaster: a new tool to decipher transcriptional regulatory networks.

Wrzodek C, Schröder A, Dräger A, Wanke D, Berendzen KW, Kronfeld M, Harter K, Zell A.

Biosystems. 2010 Jan;99(1):79-81. doi: 10.1016/j.biosystems.2009.09.005. Epub 2009 Oct 9.

PMID:
19819296

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