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Cross-platform app for Bayesian MCMC analysis of molecular sequences BEAST (Bayesian evolutionary analysis sampling trees) is a free and open source application for evolutionary inference from molecular sequences.BEAST is a cross-platform app for Bayesian MCMC analysis of molecular sequences. BEAST is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models.BEAST 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 to average over tree space, so that each tree is weighted proportional to its posterior probability. Here are some key features of "BEAST": · Constant rate molecular clock models. · This is the default model. The tree can be calibrated by specifying a mutation rate. · Variable rate (relaxed) molecular clock models. · Implements the uncorrelated relaxed clock models of Drummond, Ho, Phillips & Rambaut (2006, PLoS Biology) see below for full citation. · Divergence date estimates. · Dates of divergence for specific most recent common ancestors (MRCA) can be estimated. · Non-contemporaneous sequences (!TipDate) molecular clock models. · When the differences in the dates associated with the sequences comprise a significant proportion of the age of the entire tree, these dates can be incorporated into the model providing a source of information about the rate of substitution. · Substitution model heterogeneity across sites. · Different substitution models can be specified for different sets of sites. For example, each codon position can be allowed a different substitution matrix and gamma model of rate heterogeneity. · Flexible model specification. · The model-specification file format allows considerable flexibility. For example, it is possible to specify that each codon position has a different rate, a different degree of rate heterogeneity but the same transition/transversion ratio. · Range of substitution models. · BEAST (Bayesian evolutionary analysis sampling trees) is a free and open source application for evolutionary inference from molecular sequences. · Flexible choice of priors on parameters. · Any parameter can be given a prior. For example, the age of the root of the tree can be given an exponential prior with a given mean. · Coalescent models of population size and growth. · Various models of coalescent population growth can be used. At present, constant size and exponential growth are available but more will be added soon. These models basically act as priors on the ages of nodes in the tree but the parameters (population size and growth rate) can be sampled and estimated. · Multi-locus coalescent models. · Two unlinked genes can be given the same coalescent population model but a different substitution process and tree, allowing the production of multi-locus coalescent inference. · Local clock molecular clock models. · Allowing different clades in the tree to have different rates (or indeed, completely different substitution processes). What's New in This Release: New Features: · GUI versions of BEAST show a dialog box to set various options that are otherwise only available by command-line. Bug Fixes: · Issue 55: MCMC Screen log doesn't currently work. · Issue 70: beauty and partition into codon positions · Issue 72: Beauti should hard limit GTR model parameters · Issue 122: Ctrl-A in Beauti -> Exception · Issue 127: BEAUTi prior panel, prior upper and lower does not show · INFINITY · Issue 128: BEAUTi: tree prior Logistic Growth is not available for · calibration · Issue 146: BEAUTi: binary COVARION model · Issue 169: Editing the file name stem in BEAUti causes the insertion · point to jump to the end · Issue 173: BEAUTi: partially link exception · Issue 181: BEAUTi: need enhancement to default behaviour when adding · additional alignment after unlinking all · Issue 193: Improved convergence diagnostic: compute effective size of · combined runs by concatenating the samples · Issue 194: BEAUTi: prior setting exception when changing value · Issue 199: Tracer shows only first log file entry when multiples · entries have the same name · Issue 201: Editing file name stem in MCMC panel causes insertion point · to jump to end · Issue 202: Build scripts producing JDK 1.6 classes so distribution fails · on machines with JDK 1.5 · Issue 203: Launch4j bug affecting the link of NucleotideLikelihoodCore.dll · Issue 204: BEAUTi: tree prior Constant Size is not working for node calibration · Issue 205: Tittle information disappeared in the console using windows · paramter to run BEAST · Issue 209: pathogen dose not compile · Issue 211: BEAUTi: Amino Acid site model xml is wrong · Issue 212: BEAST Linux version: need chmod 755 * · Issue 215: Default memory allocations for Mac packaging are too small · Issue 216: Default memory allocations for Linux packaging are too small · Issue 217: Problems with the Mac OS X packaging · Issue 218: BeastMain options dialog giving error "Illegal entry value · must be between 1 and 21474863647" · Issue 220: The shell scripts to launch BEAST in command line can't cope · with spaces in the path. · Issue 221: Reweight the substitution model operators in BEAUti · Issue 222: Naming of 'treeLikelihood' when only 1 partition · Issue 223: Set the 'operator analysis' file name as an attribute in · MCMC element · Issue 225: TreePartitionCoalescent is not existing · Issue 226: The parsers in release_parsers.properties need to be updated · Issue 227: Fix BeastDoc to generate tag doc for BEAST users · Issue 229: Another failure of testing framework · Issue 231: Delay the start of the performance measurement until after · full evaluation · Issue 232: Mac (Windows?) version of BEAST closes console on error · Issue 234: Make the dreaded "The initial posterior is zero" error a bit · more friendly to debug · Issue 236: dr.evomodel.operators.TraitGibbsOperator is duplicated with · parsers in either release_parser.properties or BeastParser.java · Issue 237: BEAUTi: taxon set not handling multi-tree partition · Issue 238: Naming of 'patterns' when only 1 partition · Issue 240: BEAUTi: useAmbiguities of treeLikelihood should be default · as true for binay Covarion · Issue 242: BEAUTi: create a check box to choose useAmbiguities in · treeLikelihood for binary data · Issue 244: URGENT: Default prior review · Issue 247: BEAUTi: wrong XML in frequecies choosing EMPIRICAL binary · COVARION model · Issue 248: BEAUTi exception (*BEAST) when linking some same taxa for a · tree model by given different taxa in total · Issue 250: BEAUTi: wrong alignment blocks for multi-gene when choosing · "create empty alignment" · Issue 253: BEAUTi add a pop-up box to check the default priors when · click Generate BEAST file · Issue 254: BEAUTi generate XML button should be disable after all data · partition removed · Issue 255: Turn off parser WARNINGs by default for released version · Issue 256: BEAUTi: Add comment in XML "skyride.logPopSize is log unit · unlike other popSize" · Issue 257: BEAUTi: Binary data and multiple partitions does not generate · the siteModel correctly · Issue 259: BEAUTi: Mac OS MCMC panel problem · Issue 260: BEAUTi: correct English · Issue 261: Error parsing element with id null · Issue 262: wrong XML of testCataclysmCoalescent.xml · Issue 264: ImportException: Number format error for

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