(Q33495765)

27 July 2017

title

Phylogenetic inference under varying proportions of indel-induced alignment gaps (English)

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27 July 2017

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Bhakti Dwivedi

1

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author name string

Sudhindra R Gadagkar

series ordinal

2

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27 July 2017

publication date

23 August 2009

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27 July 2017

published in

BMC Evolutionary Biology

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27 July 2017

volume

9

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27 July 2017

page(s)

211

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Among-site rate variation and its impact on phylogenetic analyses

27 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=2746219

Probabilistic phylogenetic inference with insertions and deletions

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity

21 June 2018

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Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

21 June 2018

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Incorporating gaps as phylogenetic characters across eight DNA regions: ramifications for North American Psoraleeae (Leguminosae).

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

PAML 4: phylogenetic analysis by maximum likelihood

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice.

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Human-specific insertions and deletions inferred from mammalian genome sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Exploring the relationship between sequence similarity and accurate phylogenetic trees.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Missing data and the design of phylogenetic analyses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Evolutionary models for insertions and deletions in a probabilistic modeling framework

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Phylogenomics of eukaryotes: impact of missing data on large alignments

21 June 2018

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Phylogeny and evolution of the Australo-Papuan honeyeaters (Passeriformes, Meliphagidae)

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trnD in interspecific studies of plants

21 June 2018

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Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Selective constraints on intron evolution in Drosophila

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

MrBayes 3: Bayesian phylogenetic inference under mixed models

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Missing data, incomplete taxa, and phylogenetic accuracy

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

MRBAYES: Bayesian inference of phylogenetic trees

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

PAML: a program package for phylogenetic analysis by maximum likelihood

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

DNA assembly with gaps (Dawg): simulating sequence evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Is it better to add taxa or characters to a difficult phylogenetic problem?

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

On the best evolutionary rate for phylogenetic analysis.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Whole-Genome Analysis of Photosynthetic Prokaryotes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2746219

Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well

31 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

Efficiencies of maximum likelihood methods of phylogenetic inferences when different substitution models are used.

1 reference

12 December 2020

The relative performance of indel-coding methods in simulations

1 reference

12 December 2020

Evolutionary rates of insertion and deletion in noncoding nucleotide sequences of primates

1 reference

12 December 2020

Multiple Sequence Alignment Accuracy and Phylogenetic Inference

1 reference

12 December 2020

Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2148-9-211

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Dimensions Publication ID

27 July 2017

0 references

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27 July 2017

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