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- BEAST Software - Bayesian Evolutionary Analysis Sampling Trees | BEAST . . .
What is BEAST? BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models
- First Tutorial | BEAST Documentation
Running BEAST for the first time This tutorial will guide you through running BEAST and some of its accessory programs to do a simple phylogenetic analysis If you haven’t already, download and install BEAST following these instructions
- FigTree | BEAST Documentation
FigTree is a program for viewing trees, including summary information produced by TreeAnnotator, and producing publication quality figures
- BEAST v1. 10. 4 released | BEAST Documentation
BEAST v1 10 4 fixes a bug when trying to specify a burnin on the command line version of LogCombiner It also introduces two new command line options specific to BEAGLE v3 1 (-beagle_threading_off and -beagle_thread_count)
- BEAST X (v10. 5. 0-beta5) released | BEAST Documentation
BEAST X is the new name for BEAST v1 project and the first release version of this is v10 5 0 which supersedes v1 10 4 in the old version system From now on we will use the full major, minor, bugfix style of semantic versioning
- Frequently Asked Questions | BEAST Documentation
BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology BEAST uses MCMC
- Markov Jumps and Rewards | BEAST Documentation
This realisation includes all the transitions (Markov jumps) between states along phylogenetic branches and the time (Markov rewards) spent in the states between two transitions This tutorial discusses how to estimate such quantities using stochastic mapping techniques implemented in BEAST
- How to create custom substitution models | BEAST Documentation
Custom substitution models BEAUti provides a fairly standard selection of substitution models, but BEAST can deal with a wide range of possible models through XML specification This can be done by imposing assumptions on the general time-reversible model (GTR; Tavaré, 1986) of nucleotide substitution, or on the HKY (1985) model of nucleotide substitution This how-to guide provides XML code
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