Provided by: phast_1.5+dfsg-1_amd64 
NAME
phyloBoot - Generate simulated alignment data by parametric or nonparametric
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.
EXAMPLE
(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 commadelimited 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.