CLANN: Software for inferring phylogenetic supertrees.

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

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