Bayesian phylogenetic inference from animal mitochondrial genome arrangements

Keywords

Phylogenetic tree, Markov chain Monte Carlo, Evolutionary biology, Inference, Bayesian probability

References

• Statistical inference of phylogeniesJoseph Felsenstein — 1983
• Computational molecular biology : an algorithmic approachPavel A. Pevzner — 2000
• A Faster and Simpler Algorithm for Sorting Signed Permutations by ReversalsHaim Kaplan, Ron Shamir, Robert E. Tarjan — 1999
• Faster and simpler algorithm for sorting signed permutations by reversalsHaim Kaplan, Ron Shamir, Robert E. Tarjan — 1997
• Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.Ziheng Yang, Bruce Rannala — 1997
• The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa.Kevin G. Helfenbein, Wesley M. Brown, Jeffrey L. Boore — 2001
• Evidence from 18S ribosomal DNA that the lophophorates are protostome animalsKenneth M. Halanych, John D. Bacheller, Anna Marie A. Aguinaldo — 1995
• Gene Order Breakpoint Evidence in Animal Mitochondrial PhylogenyMathieu Blanchette, Takashi Kunisawa, David Sankoff — 1999
• Evidence for a clade of nematodes, arthropods and other moulting animalsAnna Marie A. Aguinaldo, James M. Turbeville, Lawrence S. Linford — 1997
• Phylogenetic Invariants for Genome RearrangementsDavid Sankoff, Mathieu Blanchette — 1999
• The number of evolutionary treesJoseph Felsenstein — 1978
• Multiple Genome Rearrangement and Breakpoint PhylogenyDavid Sankoff, Mathieu Blanchette — 1998
• Big trees from little genomes: mitochondrial gene order as a phylogenetic tool.Jeffrey L. Boore, Wesley M. Brown — 1998
• Equation of State Calculations by Fast Computing MachinesN. Metropolis, Arianna W. Rosenbluth, M. N. Rosenbluth — 1953
• Bayesian Phylogenetic Inference via Markov Chain Monte Carlo MethodsBob Mau, Michael A. Newton, Bret Larget — 1999
• Mitochondrial genomes of Galathealinum, Helobdella, and Platynereis: sequence and gene arrangement comparisons indicate that Pogonophora is not a phylum and Annelida and Arthropoda are not sister taxa.Jeffrey L. Boore, Wesley M. Brown — 2000
• Phylogenetic Tree Construction Using Markov Chain Monte CarloShuying Li, Dennis K. Pearl, Hani Doss — 2000
• Molecular data indicate the protostome affinity of brachiopods.Renaud de Rosa — 2001
• Monte Carlo Sampling Methods Using Markov Chains and Their ApplicationsW. Keith Hastings — 1970
• Bayesian Inference of Phylogeny and Its Impact on Evolutionary BiologyJohn P. Huelsenbeck, Fredrik Ronquist, Rasmus Nielsen — 2001

Cited by

• Mitochondrial genomes and their utility for the recovery of phylogeny in the HymenopteraMeng Mao — 2014
• Applications of heuristic search on phylogeny reconstruction problemsSüha Orhun Mutluergil — 2012
• Phylogeny and Ancestral Genome Reconstruction from Gene Order using Maximum Likelihood and Binary EncodingFei Hu — 2013
• Integration of Alignment and Phylogeny in the Whole-Genome EraHongtao Sun — 2015
• Methods for obtaining and analyzing whole chloroplast genome sequences.Robert K. Jansen, Linda A. Raubeson, Jeffrey L. Boore — 2005
• Probability Models for DNA Sequence EvolutionRick Durrett — 2002
• Advances in phylogeny reconstruction from gene order and content data.Bernard M. E. Moret, Tandy Warnow — 2005
• Object Oriented Data AnalysisJ. S. Marron, Ian L. Dryden — 2013
• On sampling SCJ rearrangement scenariosIstván Miklós, Sándor Z. Kiss, Éric Tannier — 2013
• Progressive Mauve: Multiple alignment of genomes with gene flux and rearrangementAaron E. Darling, Bob Mau, Nicole T. Perna — 2009
• Probabilistic models of eukaryotic evolution: time for integrationNicolas Lartillot — 2015
• Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny.Guido Fritzsch, Martin Schlegel, Peter F. Stadler — 2006
• Mauve: multiple alignment of conserved genomic sequence with rearrangements.Aaron E. Darling, Bob Mau, Frederick R. Blattner — 2004
• Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages.Guillaume Bourque, Evgeny M. Zdobnov, Peer Bork — 2005
• The complete mitochondrial genome of Micrura ignea Schwartz & Norenburg 2005 (Nemertea: Heteronemertea) and comparative analysis with other nemertean mitogenomes.Jaime González-Cueto, Mayron E. Escarraga-Fajardo, Ana Milena Lagos — 2015
• Counting and sampling SCJ small parsimony solutionsIstván Miklós, Sándor Z. Kiss, Éric Tannier — 2014
• Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera)Jimeng Hua, Ming Li, Pengzhi Dong — 2008
• The mitochondrial genome of Protohermes concolorus Yang et Yang 1988 (Insecta: Megaloptera: Corydalidae)Jimeng Hua, Ming Li, Pengzhi Dong — 2009
• Bayesian Estimation of the Number of Inversions in the History of Two ChromosomesA. York, Richard Durrett, Rasmus Nielsen — 2002
• progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and RearrangementAaron E. Darling, Bob Mau, Nicole T. Perna — 2010

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