(Q35541192)

8 August 2017

title

Phycas: software for Bayesian phylogenetic analysis (English)

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8 August 2017

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2

Mark T Holder

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8 August 2017

3

David L Swofford

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8 August 2017

Paul O Lewis

1

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8 August 2017

publication date

9 January 2015

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8 August 2017

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8 August 2017

volume

64

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8 August 2017

issue

3

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8 August 2017

page(s)

525-531

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A new look at the statistical model identification

8 August 2017

cites work

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Wagner and Dollo: a stochastic duet by composing two parsimonious solos.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Bayesian estimation of concordance among gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Improved harmonic mean estimator for phylogenetic model evidence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Bayesian model adequacy and choice in phylogenetics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

When trees grow too long: investigating the causes of highly inaccurate bayesian branch-length estimates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

A different perspective on the phylogenetic relationships of the Moxostomatini (Cypriniformes: Catostomidae) based on cytochrome-b and Growth Hormone intron sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Bayesian phylogenetics with BEAUti and the BEAST 1.7

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Bayesian random local clocks, or one rate to rule them all

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Brianaria (Psoraceae), a new genus to accommodate the Micarea sylvicola group

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Generalized mixture models for molecular phylogenetic estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Choosing among partition models in Bayesian phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Modeling compositional heterogeneity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Gene arrangement convergence, diverse intron content, and genetic code modifications in mitochondrial genomes of sphaeropleales (chlorophyta)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Putting incertae sedis taxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae, Chlorophyta).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Bayesian inference of species trees from multilocus data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Phylogeny and Taxonomy of an Enigmatic Sterile Lichen

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Probabilistic graphical model representation in phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Contrasting phylogeography of sandy vs. rocky supralittoral isopods in the megadiverse and geologically dynamic Gulf of California and adjacent areas

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Global diversification at the harsh sea-land interface: mitochondrial phylogeny of the supralittoral isopod genus Tylos (Tylidae, Oniscidea)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Phylogeny of the Archiborborinae (Diptera: Sphaeroceridae) based on combined morphological and molecular analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

The complete mitochondrial genome of an 11,450-year-old aurochsen (Bos primigenius) from Central Italy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Computing Bayes factors using thermodynamic integration.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

A general comparison of relaxed molecular clock models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

NCL: a C++ class library for interpreting data files in NEXUS format

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Polytomies and Bayesian phylogenetic inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Posterior predictive Bayesian phylogenetic model selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Phylogenetic inference rejects sporophyte based classification of the Funariaceae (Bryophyta): rapid radiation suggests rampant homoplasy in sporophyte evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Molecular systematics of Batrachoseps (Caudata, Plethodontidae) in southern California and Baja California: mitochondrial-nuclear DNA discordance and the evolutionary history of B. major.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

A phylogenetic hypothesis for Crocodylus (Crocodylia) based on mitochondrial DNA: Evidence for a trans-Atlantic voyage from Africa to the New World

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Performance-based selection of likelihood models for phylogeny estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

The evolution of defense mechanisms correlate with the explosive diversification of autodigesting Coprinellus mushrooms (Agaricales, Fungi).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Estimating the Dimension of a Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Misleading phylogenetic inferences based on single-exemplar sampling in the turtle genus Pseudemys

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Phylogenetic relationships of flesh flies in the subfamily Sarcophaginae based on three mtDNA fragments (Diptera: Sarcophagidae)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Between a rock and a hard polytomy: rapid radiation in the rupicolous girdled lizards (Squamata: Cordylidae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

The Bayesian "star paradox" persists for long finite sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

In and out of Madagascar: dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Bayesian selection of continuous-time Markov chain evolutionary models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

On the distributions of bootstrap support and posterior distributions for a star tree

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

The origin of the early differentiation of ivies (Hedera L.) and the radiation of the Asian Palmate group (Araliaceae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

The Large-Sample Distribution of the Likelihood Ratio for Testing Composite Hypotheses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Improving marginal likelihood estimation for Bayesian phylogenetic model selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

Branch-length prior influences Bayesian posterior probability of phylogeny.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYU132

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYU132

1 reference

8 August 2017

1 reference