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PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
TLDR
We propose a software package, PhyloBayes 3, which can be used for conducting Bayesian phylogenetic reconstruction and molecular dating analyses, using a large variety of amino acid replacement and nucleotide substitution models, including empirical mixtures or non-parametric models, as well as alternative clock relaxation processes. Expand
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A site- and time-heterogeneous model of amino acid replacement.
We combined the category (CAT) mixture model (Lartillot N, Philippe H. 2004) and the nonstationary break point (BP) model (Blanquart S, Lartillot N. 2006) into a new model, CAT-BP, accounting forExpand
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A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution.
Variations of nucleotidic composition affect phylogenetic inference conducted under stationary models of evolution. In particular, they may cause unrelated taxa sharing similar base composition to beExpand
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Parallel adaptations to high temperatures in the Archaean eon
Fossils of organisms dating from the origin and diversification of cellular life are scant and difficult to interpret, for this reason alternative means to investigate the ecology of the lastExpand
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MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes
TLDR
We present MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. Expand
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Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny
BackgroundTunicates represent a key metazoan group as the sister-group of vertebrates within chordates. The six complete mitochondrial genomes available so far for tunicates have revealed distinctiveExpand
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Computational and Experimental Evidence for the Evolution of a ( βα ) 8-Barrel Protein from an Ancestral Quarter-Barrel Stabilised by Disulfide Bonds
0022-2836/$ see front matter © 2010 E *Corresponding authors. R. Sterner Institute of Biophysics and Physical University of Regensburg, Universit Regensburg, Germany. E-mail addreExpand
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Computational and experimental evidence for the evolution of a (beta alpha)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds.
The evolution of the prototypical (beta alpha)(8)-barrel protein imidazole glycerol phosphate synthase (HisF) was studied by complementary computational and experimental approaches. The 4-foldExpand
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Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era.
Due to the lack of macromolecular fossils, the enzymatic repertoire of extinct species has remained largely unknown to date. In an attempt to solve this problem, we have characterized a cyclaseExpand
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ProCARs: Progressive Reconstruction of Ancestral Gene Orders
TLDR
We present a new homology-based method that uses a progressive approach for both the detection and the assembling of ancestral contiguity features into CARs. Expand
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