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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting treeExpand
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Phylogeny.fr: robust phylogenetic analysis for the non-specialist
TLDR
Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, phylogenetic reconstruction and the graphical representation of the inferred tree. Expand
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SMS: Smart Model Selection in PhyML
Abstract Model selection using likelihood-based criteria (e.g., AIC) is one of the first steps in phylogenetic analysis. One must select both a substitution matrix and a model for rates across sites.Expand
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FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program
TLDR
FastME provides distance algorithms to infer phylogenies, while remaining as fast as Neighbor Joining. Expand
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Genomics, biogeography, and the diversification of placental mammals
Previous molecular analyses of mammalian evolutionary relationships involving a wide range of placental mammalian taxa have been restricted in size from one to two dozen gene loci and have notExpand
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Characterization of 43 Non-Protein-Coding mRNA Genes in Arabidopsis, Including the MIR162a-Derived Transcripts1[W]
Messenger RNAs that do not contain a long open reading frame (ORF) or non-protein-coding RNAs (npcRNAs) are an emerging novel class of transcripts. Their functions may involve the RNA molecule itselfExpand
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Analyses of Phylogenetics and Evolution
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PhySIC_IST: cleaning source trees to infer more informative supertrees
TLDR
The paper introduces and tests two new methodologies, PhySIC_IST and STC, that demonstrate the interest in inferring non-plenary supertrees as well as preprocessing the source trees. Expand
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NGPhylogeny.fr: new generation phylogenetic services for non-specialists
Abstract Phylogeny.fr, created in 2008, has been designed to facilitate the execution of phylogenetic workflows, and is nowadays widely used. However, since its development, user needs have evolved,Expand
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TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
TLDR
This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. Expand
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