clann
CLANN: Software for inferring phylogenetic supertrees.
What is clann?
Clann (the Irish word for “family”), is a free software program designed and written by Chris Creevey at the Bioinformatics and Molecular Evolution Unit at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of input source trees.
Where has clann been described?
Creevey C. J. and McInerney, J. O. (2005) Clann: Investigating phylogenetic information through supertree analyses. Bioinformatics 21 (3): 390-2. pdf
Creevey C.J., Fitzpatrick DA, Philip GK, Kinsella RJ, O’connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO. (2004) Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc R Soc Lond B Biol Sci. 271(1557):2551-8. pdf
Where else have we used clann?
Philip, G.K., Creevey, C.J. and McInerney, J.O. (2005). The Opisthokonta and the Ecdysozoa may not be Clades: Stronger Support for the Grouping of Plant and Animal than for Animal and Fungi and Stronger Support for the Coelomata than Ecdysozoa. Molecular Biology and Evolution 22, 1175-1184. pdf
Fitzpatrick, D.A., Creevey, C.J. and McInerney, J.O. (2006). Genome Phylogenies Indicate a Meaningful alpha-Proteobacterial Phylogeny and Support A Grouping of the Mitochondria With the Rickettsiales. Molecular Biology and Evolution 23(1):74-85.pdf
Pisani, D., Cotton, J.A. and McInerney, J.O. (2007). Supertrees Disentangle The Chimeric Origin of Eukaryotic genomes. Molecular Biology and Evolution24(8):1752-1760. pdf
Program and manual
You can download the source code and the manual here.
A short primer describing the use of clann:
Creevey, C.J. and McInerney, J.O. (2009) Trees from Trees: Constructing Phylogenetic Supertrees Using CLANN. In: DNA sequence analysis, Ed. David Posada. Humana Press. 537:139-161. pdf
Recent papers that cite CLANN:
Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer Author(s): Creevey Christopher J.; Doerks Tobias; Fitzpatrick David A.; et al. PLOS ONE Volume: 6 Issue: 8 Article Number: e22099 DOI: 10.1371/journal.pone.0022099 Published: AUG 5 2011
An experimental study of Quartets MaxCut and other supertree methods Author(s): Swenson M. Shel; Suri Rahul; Linder C. Randal; et al. ALGORITHMS FOR MOLECULAR BIOLOGY Volume: 6 Article Number: 7 DOI: 10.1186/1748-7188-6-7 Published: APR 19 2011
Phylogenomics-Based Reconstruction of Protozoan Species Tree Author(s): Ocana Kary A. C. S.; Davila Alberto M. R. EVOLUTIONARY BIOINFORMATICS Volume: 7 Pages: 107-121 DOI: 10.4137/EBO.S6861 Published: 2011
Performance of Matrix Representation with Parsimony for Inferring Species from Gene Trees Author(s): Wang Yuancheng; Degnan James H. STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY Volume: 10 Issue: 1 Article Number: 21 DOI: 10.2202/1544-6115.1611 Published: 2011
Comparative Performance of Supertree Algorithms in Large Data Sets Using the Soapberry Family (Sapindaceae) as a Case Study Author(s): Buerki Sven; Forest Felix; Salamin Nicolas; et al. SYSTEMATIC BIOLOGY Volume: 60 Issue: 1 Pages: 32-44 DOI: 10.1093/sysbio/syq057 Published: JAN 2011
Molecular and morphometric characterisation of Xiphinema globosum Sturhan, 1978 (Nematoda: Longidoridae) from Spain Author(s): Cantalapiedra-Navarrete Carolina; Gutierrez-Gutierrez Carlos; Landa Blanca B.; et al. NEMATOLOGY Volume: 13 Pages: 17-28 DOI: 10.1163/138855410X500046 Part: Part 1 Published: 2011
A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction Author(s): Rasmussen Matthew D.; Kellis Manolis MOLECULAR BIOLOGY AND EVOLUTION Volume: 28 Issue: 1 Pages: 273-290 DOI: 10.1093/molbev/msq189 Published: JAN 2011
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets Author(s): Kupczok Anne; Schmidt Heiko A.; von Haeseler Arndt ALGORITHMS FOR MOLECULAR BIOLOGY Volume: 5 Article Number: 37 DOI: 10.1186/1748-7188-5-37 Published: DEC 6 2010
Quartets MaxCut: A Divide and Conquer Quartets Algorithm Author(s): Snir Sagi; Rao Satish IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS Volume: 7 Issue: 4 Pages: 704-718 DOI: 10.1109/TCBB.2008.133 Published: OCT-DEC 2010
DEFENSE EVOLUTION IN THE GRACILARIACEAE (RHODOPHYTA): SUBSTRATE-REGULATED OXIDATION OF AGAR OLIGOSACCHARIDES IS MORE ANCIENT THAN THE OLIGOAGAR-ACTIVATED OXIDATIVE BURST Author(s): Weinberger Florian; Guillemin Marie-Laure; Destombe Christophe; et al. JOURNAL OF PHYCOLOGY Volume:46 Issue: 5 Pages: 958-968 DOI: 10.1111/j.1529-8817.2010.00887.x Published: OCT 2010
