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Article
Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments
Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their e...
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Article
Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria
Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochon...
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Article
Ancestral state reconstruction with large numbers of sequences and edge-length estimation
Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that...
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Protocol
Looking for Darwin in Genomic Sequences: Validity and Success Depends on the Relationship Between Model and Data
Codon substitution models (CSMs) are commonly used to infer the history of natural section for a set of protein-coding sequences, often with the explicit goal of detecting the signature of positive Darwinian s...
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Article
Molecular clocks provide little information to date methanogenic Archaea
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Article
Open AccessNuclear genetic codes with a different meaning of the UAG and the UAA codon
Departures from the standard genetic code in eukaryotic nuclear genomes are known for only a handful of lineages and only a few genetic code variants seem to exist outside the ciliates, the most creative group...
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Article
Open AccessDefining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture
Assessing protein modularity is important to understand protein evolution. Still the question of the existence of a sub-domain modular architecture remains. We propose a graph-theory approach with significance...
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Article
The Site-Wise Log-Likelihood Score is a Good Predictor of Genes under Positive Selection
The strength and direction of selection on the identity of an amino acid residue in a protein is typically measured by the ratio of the rate of non-synonymous substitutions to the rate of synonymous substituti...
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Article
Open AccessOn the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations
Phylogenetic reconstruction methods based on gene content often place all the parasitic and endosymbiotic eubacteria (parasites for short) together in a clan. Many other lines of evidence point to this parasit...
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Article
Open AccessPROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis
The covarion hypothesis of molecular evolution holds that selective pressures on a given amino acid or nucleotide site are dependent on the identity of other sites in the molecule that change throughout time, ...
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Protocol
Statistical Analysis of Expressed Sequence Tags
Expressed sequence tag (EST) surveys are an efficient way to characterize large numbers of genes from an organism. The rate of gene discovery in an EST survey depends on the degree of redundancy of the cDNA li...
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Article
Open AccessA class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny
Widely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT) or Whelan and Goldman (WAG) models, are based on empirical amino acid interchange matrices estimated from databases of prot...
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Article
Topological Estimation Biases with Covarion Evolution
Covarion processes allow changes in evolutionary rates at sites along the branches of a phylogenetic tree. Covarion-like evolution is increasingly recognized as an important mode of protein evolution. Several ...
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Article
Biases in Phylogenetic Estimation Can Be Caused by Random Sequence Segments
We consider the effects of fully or partially random sequences on the estimation of four-taxon phylogenies. Fully or partially random sequences occur when whole subsets of sequences or some sites for subsets o...
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Article
Statistical informatics: software tools for statistical inference about expression arrays
