(Q44275037)

1 December 2017

title

Inference of molecular homology and sequence alignment by direct optimization (English)

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1 December 2017

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Matthew J Morgan

1

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1 December 2017

Scot A Kelchner

series ordinal

2

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1 December 2017

language of work or name

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2 April 2010

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Molecular Phylogenetics and Evolution

1 December 2017

published in

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1 December 2017

volume

56

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1 December 2017

issue

1

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1 December 2017

page(s)

305-311

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Exploring data interaction and nucleotide alignment in a multiple gene analysis of Ips (Coleoptera: Scolytinae).

1 December 2017

cites work

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Optimal Intron Analyses in the Trimeresurus Radiation of Asian Pitvipers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Concepts and tests of homology in the cladistic paradigm

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Distinguishing between convergence and parallelism is central to comparative biology: a reply to Williams and Ebach

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Homology a personal view on some of the problems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Characters, states, and homology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Phylogenetics of the lizard genus Tropidurus (Squamata: Tropiduridae: Tropidurinae): direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Alignment-ambiguous nucleotide sites and the exclusion of systematic data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Characterizing regions of ambiguous alignment caused by the expansion and contraction of hairpin-stem loops in ribosomal RNA molecules.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Data exploration in phylogenetic inference: scientific, heuristic, or neither

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Transformation Series as an Ideographic Character Concept

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

The accuracy of ribosomal RNA comparative structure models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Signal, Noise, and Reliability in Molecular Phylogenetic Analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Tracing the decay of the historical signal in biological sequence data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Aligned 18S and insect phylogeny.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Opinions on multiple sequence alignment, and an empirical comparison of repeatability and accuracy between POY and structural alignment.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

From conviction to anti-superfluity: old and new justifications of parsimony in phylogenetic inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

When does homology mean something else?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

When it comes to homology, bad habits die hard.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family sarcocystidae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

An empirical test of the treatment of indels during optimization alignment based on the phylogeny of the genus Secale (Poaceae).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Multiple sequence alignment in phylogenetic analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Molecular phylogenetics of the Meteoriaceae s. str.: focusing on the genera Meteorium and Papillaria

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

"Homology" in proteins and nucleic acids: a terminology muddle and a way out of it.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

The merits of similarity reconsidered

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Independence of alignment and tree search.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Mantophasmatodea and phylogeny of the lower neopterous insects

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Molecular homology assessment and phylogeny in the lizard family opluridae (Squamata: Iguania).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

OPTIMIZATION ALIGNMENT: THE END OF MULTIPLE SEQUENCE ALIGNMENT IN PHYLOGENETICS?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Loss and recovery of wings in stick insects

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

18S ribosomal RNA and tetrapod phylogeny

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2010.03.032

10.1016/J.YMPEV.2010.03.032

7 January 2021

Identifiers

DOI

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1 December 2017

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