Evidence of absence treated as absence of evidence: The effects of variation in the number and distribution of gaps treated as missing data on the results of standard maximum likelihood analysis

[Display omitted] •Likelihood scores vary negatively with gap opening cost and amount of missing data.•Negative relationship due to altered nucleotide homologies, not missing data per se.•Effect of alignment parameters and missing data on topology is unpredictable. Although numerous studies have dem...

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Veröffentlicht in:	Molecular phylogenetics and evolution 2021-01, Vol.154, p.106966-106966, Article 106966
Hauptverfasser:	Jacob Machado, Denis, Castroviejo-Fisher, Santiago, Grant, Taran
Format:	Artikel
Sprache:	eng
Schlagworte:	Alignment Ambiguous characters Databases, Genetic Indel Likelihood Functions Maximum likelihood Missing data Monte Carlo Method Nucleotides - genetics Phylogenetic analysis Phylogeny Reference Standards Sequence Alignment
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