(Q33904603)

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Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data

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scholarly article

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Europe PubMed Central

29 July 2017

Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data (English)

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Europe PubMed Central

29 July 2017

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Akifumi S Tanabe

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Akifumi S Tanabe

1

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publication date

19 May 2011

1 reference

Europe PubMed Central

29 July 2017

Molecular Ecology Resources

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Europe PubMed Central

29 July 2017

11

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Europe PubMed Central

29 July 2017

914-921

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Europe PubMed Central

29 July 2017

5

1 reference

Europe PubMed Central

29 July 2017

ProtTest: selection of best-fit models of protein evolution

1 reference

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MtArt: A New Model of Amino Acid Replacement for Arthropoda

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Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA.

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A new look at the statistical model identification

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The evolution of alternative parasitic life histories in large blue butterflies

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A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution

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A site- and time-heterogeneous model of amino acid replacement.

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Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders

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A new genus of African monkey, Rungwecebus: morphology, ecology, and molecular phylogenetics

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Evolutionary trees from DNA sequences: A maximum likelihood approach

1 reference

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Single origin of a pan-Pacific bird group and upstream colonization of Australasia

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Early evolution of the venom system in lizards and snakes

1 reference

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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

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Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

1 reference

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Amino acid substitution matrices from protein blocks

1 reference

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21 January 2018

Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I.

1 reference

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Mitochondrial protein phylogeny joins myriapods with chelicerates.

1 reference

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RETRACTED: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

1 reference

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MAFFT version 5: improvement in accuracy of multiple sequence alignment

1 reference

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Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

1 reference

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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

1 reference

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Estimation of evolutionary distances between homologous nucleotide sequences

1 reference

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21 January 2018

Different versions of the Dayhoff rate matrix

1 reference

https://api.crossref.org/works/10.1111%2FJ.1755-0998.2011.03021.X

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

1 reference

https://api.crossref.org/works/10.1111%2FJ.1755-0998.2011.03021.X

21 January 2018

An improved general amino acid replacement matrix

1 reference

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Heterotachy, an important process of protein evolution

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Kerrighed: A Single System Image Cluster Operating System for High Performance Computing

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Molecular phylogenetics and the origins of placental mammals

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HIV-specific probabilistic models of protein evolution

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Bayesian phylogenetic analysis of combined data

1 reference

https://api.crossref.org/works/10.1111%2FJ.1755-0998.2011.03021.X

21 January 2018

On the conservation of protein sequences in evolution

1 reference

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21 January 2018

Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

1 reference

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jModelTest: phylogenetic model averaging

1 reference

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21 January 2018

MODELTEST: testing the model of DNA substitution

1 reference

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Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

1 reference

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Does choice in model selection affect maximum likelihood analysis?

1 reference

https://api.crossref.org/works/10.1111%2FJ.1755-0998.2011.03021.X

21 January 2018

MrBayes 3: Bayesian phylogenetic inference under mixed models

1 reference

https://api.crossref.org/works/10.1111%2FJ.1755-0998.2011.03021.X

21 January 2018

Estimating the Dimension of a Model

1 reference

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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

1 reference

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Further analysts of the data by akaike' s information criterion and the finite corrections

1 reference

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A transition probability model for amino acid substitutions from blocks.

1 reference

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A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

1 reference

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21 January 2018

Maximum-Likelihood Models for Combined Analyses of Multiple Sequence Data

1 reference

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PAML 4: phylogenetic analysis by maximum likelihood

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Estimation of evolutionary distances between nucleotide sequences.

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rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny

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The Biasing Effect of Compositional Heterogeneity on Phylogenetic Estimates May be Underestimated

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Identifiers

10.1111/J.1755-0998.2011.03021.X

1 reference

Europe PubMed Central

29 July 2017

1 reference

Europe PubMed Central

29 July 2017

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