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
Click here for Google Code Site
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:
Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. P Skoglund, H Malmstrm, M Raghavan, J Stor, P Hall – Science, 2012.
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. SC Di Rienzi, I Sharon, KC Wrighton, O Koren, LA Hug – Elife, 2013.
Genome-wide comparative analysis of phylogenetic trees: the prokaryotic forest of life. P Puigb, YI Wolf, EV Koonin – Evolutionary Genomics, 2012
SuperFine: fast and accurate supertree estimation. MS Swenson, R Suri, CR Linder – Systematic …, 2012
Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals. X Zhou, S Xu, J Xu, B Chen, K Zhou – Systematic …, 2012
Universal pacemaker of genome evolution. S Snir, YI Wolf, EV Koonin – 2012
A Bayesian approach for fast and accurate gene tree reconstruction. MD Rasmussen, M Kellis – Molecular Biology and Evolution, 2011
Supertrees based on the subtree prune-and-regraft distance. C Whidden, N Zeh, RG Beiko – Systematic biology, 2014
Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis. D Bogumil, D AlvarezPonce, G Landan – Molecular biology and …, 2013
Comparative transcriptomics of early dipteran development. E JimnezGuri, J HuertaCepas, L Cozzuto – Bmc …, 2013
[HTML] Reconstruction of family-level phylogenetic relationships within Demospongiae (Porifera) using nuclear encoded housekeeping genes. MS Hill, AL Hill, J Lopez, KJ Peterson, S Pomponi – PLoS One, 2013
The impact of HGT on phylogenomic reconstruction methods. P Lapierre, E LasekNesselquist – Briefings in …, 2014
Horizontal gene transfer drives extreme physiological change in Haloarchaea. C Creevey, J McInerney – arXiv preprint arXiv:1209.2455, 2012
Fast local search for unrooted Robinson-Foulds supertrees. R Chaudhary, JG Burleigh – … /ACM Transactions on, 2012
Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data. KA Johnson, BR Holland, MM Heslewood – Molecular Phylogenetics …, 2012
Diversity and evolution of ectomycorrhizal host associations in the Sclerodermatineae (Boletales, Basidiomycota). AW Wilson, M Binder, DS Hibbett – New Phytologist, 2012
Comparative geno-plasticity analysis of Mycoplasma bovis HB0801 (Chinese isolate). J Qi, A Guo, P Cui, Y Chen, R Mustafa, X Ba, C Hu – PLoS One, 2012
Universally distributed single-copy genes indicate a constant rate of horizontal transfer CJ Creevey, T Doerks, DA Fitzpatrick, J Raes, P Bork – PLoS One, 2011
Consensus and Confusion in Molluscan Trees: Evaluating Morphological and Molecular Phylogenies. JD Sigwart, DR Lindberg – Systematic biology, 2014
An introduction to supertree construction (and partitioned phylogenetic analyses) with a view toward the distinction between gene trees and species trees. ORP BinindaEmonds – … Comparative Methods and Their Application in …, 2014
Low-parameter phylogenetic inference under the general Markov model. BR Holland, PD Jarvis, JG Sumner – Systematic biology, 2013
The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements. J Feng, B Liu, Z Zhang, Y Ren, Y Li, F Gan, Y Huang – PloS one, 2012
Multiple Groups of Endogenous Epsilon-Like Retroviruses Conserved across Primates. K Brown, RD Emes, RE Tarlinton – Journal of virology, 2014
An experimental study of Quartets MaxCut and other supertree methods. MS Swenson, R Suri, CR Linder – Algorithms for Molecular …, 2011
Lactobacillus ruminis strains cluster according to their mammalian gut source. MM ODonnell, HMB Harris, DB Lynch – BMC …, 2015
Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics. WA Akanni, M Wilkinson – Royal Society …, 2015
Mitochondrial data are not suitable for resolving placental mammal phylogeny. CC Morgan, CJ Creevey, MJ OConnell – Mammalian Genome, 2014
LU St: a tool for approximated maximum likelihood supertree reconstruction. WA Akanni, CJ Creevey, M Wilkinson – BMC …, 2014
Fossil gaps inferred from phylogenies alter the apparent nature of diversification in dragonflies and their relatives. RB Davis, DB Nicholson, ELR Saunders – BMC Evolutionary …, 2011
Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom. EM Medina, GW Jones, DA Fitzpatrick – Journal of molecular evolution, 2011
Comparative performance of supertree algorithms in large data sets using the soapberry family (Sapindaceae) as a case study. S Buerki, F Forest, N Salamin – Systematic …, 2011
Determining the culturability of the rumen bacterial microbiome. CJ Creevey, WJ Kelly, G Henderson – Microbial …, 2014
Phylogenomics Enabling Genome-Based Mycology. JE Stajich – Systematics and Evolution, 2015
The structure of natural microbial enemy-victim networks. T Poisot, M Lounnas, ME Hochberg – Ecological Processes, 2013
Identifying single copy orthologs in Metazoa. CJ Creevey, J Muller, T Doerks, JD Thompson – PLoS Comput Biol, 2011
Modularized evolution in archaeal methanogens phylogenetic forest. J Li, CF Wong, MT Wong, H Huang – Genome biology and …, 2014
Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins. CC Staats, Junges, RL Guedes – BMC …, 2014
Quartet decomposition server: a platform for analyzing phylogenetic trees. F Mao, D Williams, O Zhaxybayeva – BMC …, 2012
Cleaning wrasse species vary with respect to dependency on the mutualism and behavioural adaptations in interactions. L Barbu, C Guinand, R Bergmller, N Alvarez – Animal Behaviour, 2011
Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios. VA Lyubetsky, LI Rubanov, LY Rusin – Biology direct, 2012
An Orthology-Based Analysis of Pathogenic Protozoa Impacting Global Health: An Improved Comparative Genomics Approach with Prokaryotes and Model Eukaryote …
RRC Cuadrat, SM da Serra Cruz – Omics: a journal of …, 2014
Body size evolution in Titanosauriformes (Sauropoda, Macronaria). LM Souza, RM Santucci – Journal of evolutionary biology, 2014
EM for phylogenetic topology reconstruction on nonhomogeneous data. E IbezMarcelo, M Casanellas – BMC evolutionary biology, 2014
A phylogeny of Bromeliaceae (Poales, Monocotyledoneae) derived from an evaluation of nine supertree methods. J ESCOBEDOSARTI, I RAMREZ – … of Systematics and …, 2013
Performance of matrix representation with parsimony for inferring species from gene trees. Y Wang, JH Degnan – Statistical Applications in Genetics and …, 2011
Molecular phylogeny of the diverse parasitoid wasp genus Ophion Fabricius (Hymenoptera: Ichneumonidae: Ophioninae). MD SCHWARZFELD, GR BROAD – Systematic …, 2015
Molecular evolution and phylogeny of methanogenic archael genomes. J Li – 2014
Conventional simulation of Biological sequences Leads to a Biased Assessment of Multi-Loci phylogenetic Analysis. BO Aguiar, CG Schrago – Evolutionary bioinformatics online, 2013
Couplet supertree by equivalence partitioning of taxa set and dag formation. S Bhattacharyya, J Mukhopadhyay – … of the 5th ACM Conference on …, 2014
Split-based computation of majority-rule supertrees. A Kupczok – BMC evolutionary biology, 2011
Molecular and morphometric characterisation of Xiphinema globosum Sturhan, 1978 (Nematoda: Longidoridae) from Spain. C CantalapiedraNavarrete – …, 2011
Algorithms for constructing more accurate and inclusive phylogenetic trees. R Chaudhary – 2013
Phylogenomics-based reconstruction of protozoan species tree. KAS Ocaa, AM Dvila – Evolutionary bioinformatics online, 2011
Phylogenomic analysis resolves the interordinal relationships. X Zhou, S Xu, J Xu, B Chen, K Zhou, G Yang – 2011
EM for phylogenetic topology reconstruction on non-homogeneous data. E Ibez, M Casanellas – arXiv preprint arXiv:1311.5557, 2013
Analysis of multiple protein sequence alignments and phylogenetic trees in the context of phylogenomics studies. SJ Capella Gutirrez – 2012
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