(Q34210170)

31 July 2017

title

Standard maximum likelihood analyses of alignments with gaps can be statistically inconsistent (English)

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31 July 2017

1 reference

1

Tandy Warnow

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31 July 2017

publication date

9 March 2012

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31 July 2017

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31 July 2017

volume

4

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31 July 2017

page(s)

RRN1308

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Treelength optimization for phylogeny estimation

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

RAxML and FastTree: comparing two methods for large-scale maximum likelihood phylogeny estimation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

The impact of multiple protein sequence alignment on phylogenetic estimation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Multiple sequence alignment: a major challenge to large-scale phylogenetics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

FastTree 2--approximately maximum-likelihood trees for large alignments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Phylogenetic inference under varying proportions of indel-induced alignment gaps

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Phylogeny estimation and alignment via POY versus Clustal + PAUP*: a response to Ogden and Rosenberg (2007).

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Incorporating indel information into phylogeny estimation for rapidly emerging pathogens

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Incorporating information from length-mutational events into phylogenetic analysis.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Joint Bayesian Estimation of Alignment and Phylogeny

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Bayesian coestimation of phylogeny and sequence alignment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

5 July 2018

1 reference

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MrBayes 3: Bayesian phylogenetic inference under mixed models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

GapCoder automates the use of indel characters in phylogenetic analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Evolutionary HMMs: a Bayesian approach to multiple alignment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Invertibility of the TKF model of sequence evolution.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

An algorithm for statistical alignment of sequences related by a binary tree.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

A probabilistic treatment of phylogeny and sequence alignment.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3299439

Alignment and Topological Accuracy of the Direct Optimization approach via POY and Traditional Phylogenetics via ClustalW + PAUP*

28 October 2018

1 reference

12 December 2020

How should gaps be treated in parsimony? A comparison of approaches using simulation

1 reference

12 December 2020

Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy

1 reference

12 December 2020

Designing fast converging phylogenetic methods

1 reference

12 December 2020

The accuracy of fast phylogenetic methods for large datasets

1 reference

12 December 2020

Identifiers

DOI

10.1371/CURRENTS.RRN1308

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31 July 2017

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31 July 2017

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