PROGRAM: phyloBoot

USAGE: phyloBoot [OPTIONS] <model_fname>|<msa_fname>

DESCRIPTION:

    Generate simulated alignment data by parametric or nonparametric
    bootstrapping, and/or estimate errors in phylogenetic model parameters.
    When estimating errors in parameters, the tree topology is not inferred
    -- estimated errors are conditional on the given topology.

    If a model is given in the form of a .mod file (<model_fname>), then
    parametric bootstrapping is performed -- i.e., synthetic data sets are
    drawn from the distribution defined by the model.  Otherwise, the input
    file is assumed to be a multiple alignment, and non-parametric
    bootstrapping is performed -- i.e., sites are drawn (with replacement)
    from the empirical distribution defined by the given alignment.  

    The default behavior is to produce simulated alignments, estimate model
    parameters for each one, and then write a table to stdout with a row
    for each parameter and columns for the mean, standard deviation
    (approximate standard error), median, minimum, and maximum of estimated
    values, plus the boundaries of 95%% and 90%% confidence intervals.  
    
    The --alignments-only option, however, allows the parameter estimation
    step to be bypassed entirely, and the program to be used simply to
    generate simulated data sets.

    See usage for phyloFit for additional details on tree-building
    options.

EXAMPLES:
    
    (See below for more details on options)

    1. Estimation of parameter errors by parametric bootstrapping.

        phyloBoot --nreps 500 --nsites 10000 mymodel.mod > par_errors

    2. Estimation of parameter errors by nonparametric bootstrapping.

        phyloBoot --nreps 500 --nsites 10000 \
            --tree "((human,chimp),(mouse,rat))" myalignment.fa > \
            nonpar_errors

    3. Parametric generation of simulated data.
    
        phyloBoot mymodel.mod --alignments-only pardata \
            --nreps 500 --nsites 10000 

    4. Nonparametric generation of simulated data.
    
        phyloBoot myalignment.fa --alignments-only nonpardata \
            --nreps 500 --nsites 10000 

OPTIONS:

 (bootstrapping options)

    --nsites, -L <number>
        Number of sites in sampled alignments.  If an alignment is
        given (non-parametric case), default is number of sites in
        alignment, otherwise default is 1000.

    --nreps, -n <number>
        Number of replicates.  Default is 100.

    --msa-format, -i FASTA|PHYLIP|MPM|MAF|SS
        (non-parametric case only)  Alignment format.  Default is to guess
	format from file contents.        

    --alignments-only, -a <fname_root>
        Generate alignments and write them to files with given filename
        root, but do not estimate parameters.  

    --dump-mods, -d <fname_root>
        Dump .mod files for individual estimated models (one for each
        replicate).

    --dump-samples, -m <fname_root>
        Dump simulated alignments to files with given filename root.
        Similar to --alignments-only but does not disable parameter
        estimation.

    --dump-format, -o FASTA|PHYLIP|MPM|SS.
        (For use with --alignments-only or --dump-samples) File format to
        use when dumping raw alignments.  Default FASTA.

    --read-mods, -R <fname_list>
        Read estimated models from list of filenames instead of generating
        alignments and estimating parameters.  fname_list can be comma-
        delimited list of files, or, if preceded by a '*', the name of a 
        file containing the file names (one per line).  Can be used to compute
        statistics for replicates that have been processed separately (see
        --alignments-only).  When this option is used, the primary argument
        to the program (<model_fname>|<msa_fname>) will be ignored.

    --output-average, -A <fname>
        Output a tree model representing the average of all input
        models to the specified file.

    --quiet, -q
        Proceed quietly.

    --help, -h
        Print this help message.

 (tree-building options)

    --tree, -t <tree_fname>|<tree_string>
        (Required if non-parametric and more than two species) Name
        of file or literal string defining tree topology.

    --subst-mod, -s JC69|F81|HKY85|REV|SSREV|UNREST|R2|R2S|U2|U2S|R3|R3S|U3|U3S
        (default REV).  Nucleotide substitution model.

    --nrates, -k <nratecats>
        (default 1).  Number of rate categories to use.  Specifying a
        value of greater than one causes the discrete gamma model for
        rate variation to be used.

    --EM, -E
        Use EM rather than the BFGS quasi-Newton algorithm for parameter
        estimation.

    --precision, -p HIGH|MED|LOW
        (default HIGH) Level of precision to use in estimating model
        parameters.

    --init-model, -M <mod_fname>
        Initialize optimization procedure with specified tree model.

    --init-random, -r
        Initialize parameters randomly.

    --scale,-P <rho>
        Scale input tree by factor rho before doing parametric simulations.

    --subtree,-S <node>
        For use with --subtree-scale and/or subtree-switch.  Define 
        subtree including all children of named node, including branch 
	leading up to node.

    --subtree-scale,-l <lambda>
        Scale subtree defined with --subtree option by factor lambda.

    --subtree-switch,-w <prob>
        With given probability, randomly switch branches in tree from
	subtree to supertree and vice versa.  Randomization is performed
	independently for each branch in every column of simulated data.

    --scale-file,-F <file>
        (For use with --subtree in parametric mode).  Instead of using 
        --subtree-scale or --scale, read in a tab-delimited file with 
        three columns: numSite,scale,subtree_scale.  For each row in the 
        file phyloBoot will simulate the given number of sites with those 
        scaling factors, and then will move on to the next row, so that the 
        total number of sites is the sum of the first column.