An improved statistical method for detecting heterotachy in nucleotide sequences.

No abstract is available for this paper.

• Publication year

  2006

• Venue

  Molecular biology and evolution

• Publication date

  2006-07-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/MOLBEV/MSL006PMID 16672284
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Heterotachy and tree building: a case study with plastids and eubacteria.

  2006cited by this paper
• Rate of change of concomitantly variable codons

  2005cited by this paper
• Likelihood, parsimony, and heterogeneous evolution.

  2005cited by this paper
• A tale of two processes.

  2005cited by this paper
• Should phylogenetic models be trying to "fit an elephant"?

  2005cited by this paper
• The European ribosomal RNA database

  2004cited by this paper
• Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous

  2004cited by this paper
• All of Statistics: A Concise Course in Statistical Inference

  2004cited by this paper
• Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.

  2004cited by this paper
• PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]

  2004cited by this paper
• Statistical significance for genomewide studies

  2003influential reference
• The positive false discovery rate: a Bayesian interpretation and the q-value

  2003influential reference
• An Empirical Analysis of mt 16S rRNA Covarion-Like Evolution in Insects: Site-Specific Rate Variation Is Clustered and Frequently Detected

  2002cited by this paper
• Heterotachy, an important process of protein evolution.

  2002influential reference
• PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10

  2002cited by this paper
• Testing a covariotide model of DNA substitution.

  2002cited by this paper
• RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.

  2001cited by this paper
• Maximum-likelihood phylogenetic analysis under a covarion-like model.

  2001influential reference
• Mathematical Elegance with Biochemical Realism: The Covarion Model of Molecular Evolution

  2001cited by this paper
• Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA.

  2001cited by this paper
• On the conservation of protein sequences in evolution.

  2001influential reference
• Molecular phylogeny: pitfalls and progress.

  2000cited by this paper
• Microsporidia: accumulating molecular evidence that a group of amitochondriate and suspectedly primitive eukaryotes are just curious fungi.

  2000cited by this paper
• On the conservation of protein sequences in evolution.

  2000cited by this paper
• Accounting for Variability in the Use of Permutation Testing to Detect Quantitative Trait Loci

  2000cited by this paper
• RNA secondary structure: physical and computational aspects

  2000cited by this paper
• Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution.

  2000cited by this paper
• Invariable sites models and their use in phylogeny reconstruction.

  2000cited by this paper
• The Root of the Tree of Life in the Light of the Covarion Model

  1999cited by this paper
• Statistical methods for testing functional divergence after gene duplication.

  1999cited by this paper
• A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages.

  1998cited by this paper
• High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA.

  1998influential reference
• Modeling the covarion hypothesis of nucleotide substitution.

  1998cited by this paper
• PAML: a program package for phylogenetic analysis by maximum likelihood

  1997cited by this paper
• Substitution rate calibration of small subunit ribosomal RNA identifies chlorarachniophyte endosymbionts as remnants of green algae.

  1996cited by this paper
• A quantitative map of nucleotide substitution rates in bacterial rRNA.

  1996cited by this paper
• Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.

  1996cited by this paper
• Among-site rate variation and its impact on phylogenetic analyses.

  1996cited by this paper
• Neighbor Joining and Maximum Likelihood with RNA Sequences: Addressing the Interdependence of Sites

  1995cited by this paper
• Controlling the false discovery rate: a practical and powerful approach to multiple testing

  1995influential reference
• A stochastic model for the evolution of autocorrelated DNA sequences.

  1994cited by this paper
• Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods.

  1992cited by this paper
• The statistical analysis of mitochondrial DNA polymorphisms: chi 2 and the problem of small samples.

  1989cited by this paper
• Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques.

  1987cited by this paper
• An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution

  1970cited by this paper

• Trichostomatid Ciliates (Alveolata, Ciliophora, Trichostomatia) Systematics and Diversity: Past, Present, and Future

  2020cites this paper
• Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda

  2019cites this paper
• GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments.

  2019cites this paper
• GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments

  2017cites this paper
• GHOST: a time-reversible mixture model for recovering phylogenetic signal from heterotachously-evolved sequence alignments

  2017cites this paper
• Causes, consequences and solutions of phylogenetic incongruence

  2015cites this paper
• Molecular Evolution and Functional Characterization of the Visual Pigment Proteins of the Great Bowerbird (Chlamydera nuchalis) and Other Vertebrates

  2013cites this paper
• Fast statistical tests for detecting heterotachy in protein evolution.

  2011cites this paper
• A test for heterotachy using multiple pairs of sequences.

  2011cites this paper
• Site-specific time heterogeneity of the substitution process and its impact on phylogenetic inference

  2011cites this paper
• Assessing the molluscan hypothesis Serialia (Monoplacophora+Polyplacophora) using novel molecular data.

  2010cites this paper
• Limited effects of among-lineage rate variation on the phylogenetic performance of molecular markers.

  2010cites this paper
• Current Approaches to Phylogenomic Reconstruction

  2010cites this paper
• A T est for Heterotac h y Using Multiple P airs of Sequences

  2010cites this paper
• Natural selection and phylogenetic analysis

  2009cites this paper
• PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

  2009cites this paper
• General heterotachy and distance method adjustments.

  2009cites this paper
• A mixed branch length model of heterotachy improves phylogenetic accuracy.

  2008cites this paper
• Animal phylogeny and large-scale sequencing: progress and pitfalls

  2008cites this paper
• Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites.

  2008cites this paper
• Building trees of algae: some advances in phylogenetic and evolutionary analysis

  2008cites this paper
• Dealing with model uncertainty in reconstructing ancestral proteins in the laboratory: examples from archosaur visual pigments and coral fluorescent proteins

  2007cites this paper
• Identifying dramatic selection shifts in phylogenetic trees

  2007cites this paper
• Evaluation of the models handling heterotachy in phylogenetic inference

  2007cites this paper
• Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

  2006cites this paper
• Short-wavelength sensitive opsin (SWS1) as a new marker for vertebrate phylogenetics

  2006cites this paper