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BEAST: Bayesian evolutionary analysis by sampling trees
TLDR
BEAST is a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree that provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. Expand
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
TLDR
The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package version 1.7 is presented, which implements a family of Markov chain Monte Carlo algorithms for Bayesian phylogenetic inference, divergence time dating, coalescent analysis, phylogeography and related molecular evolutionary analyses. Expand
BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
TLDR
BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. Expand
Relaxed Phylogenetics and Dating with Confidence
TLDR
This work describes how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times and provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. Expand
Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
TLDR
The software package Tracer is presented, for visualizing and analyzing the MCMC trace files generated through Bayesian phylogenetic inference, which provides kernel density estimation, multivariate visualization, demographic trajectory reconstruction, conditional posterior distribution summary, and more. Expand
Bayesian coalescent inference of past population dynamics from molecular sequences.
We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model ofExpand
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
TLDR
Seq-Gen is a program that will simulate the evolution of nucleotide sequences along a phylogeny, using common models of the substitution process, including the general reversible model. Expand
Comparative analysis by independent contrasts (CAIC): an Apple Macintosh application for analysing comparative data
TLDR
CAIC is an application for the Apple Macintosh which allows the valid analysis of comparative (multi-species) data sets that include continuous variables and can be analysed validly in standard statistical packages to test hypotheses about correlated evolution among traits. Expand
Bayesian Phylogeography Finds Its Roots
TLDR
It is concluded that the Bayesian phylogeographic framework will make an important asset in molecular epidemiology that can be easily generalized to infer biogeogeography from genetic data for many organisms. Expand
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
TLDR
The BEAST software package unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. Expand
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