PHYLOBOOT(1)

🌈 NAME 🌈

phyloBoot — generate simulated alignment data by parametric or nonparametric. It's a User Commands page, section 1, and honestly it's giving "I make fake data so you can test your real data" main character energy. 💅

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✨ DESCRIPTION ✨

okay so bestie, here's the whole vibe: phyloBoot generates simulated alignment data by parametric or nonparametric bootstrapping, and/or estimates errors in phylogenetic model parameters. And when it's estimating errors in parameters, heads up — the tree topology is not inferred. The estimated errors are conditional on the given topology, periodt. No take-backs, no re-guessing your tree. 🫶

Now the fork in the road, and this part matters:

• 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 (that's the approximate standard error, bestie), median, minimum, and maximum of estimated values, plus the boundaries of 95% and 90% confidence intervals. It's a whole little spreadsheet, she ate. 😌

The --alignments-only option, however, lets the parameter estimation step be bypassed entirely, and the program to be used simply to generate simulated data sets. And if you want more on tree-building options, go see the usage for phyloFit. 👑

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🦋 EXAMPLE 🦋

(See below for more details on options — like, genuinely, they're right there.)

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

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💖 OPTIONS 💖

🎀 bootstrapping options 🎀

• --nsites, -L <number> — Number of sites in sampled alignments. If an alignment is given (that's the non-parametric case, babe), 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. She's intuitive like that. 🔮
• --alignments-only, -a <fname_root> — Generate alignments and write them to files with given filename root, but do not estimate parameters. Just vibes, no math. 💅
• --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 a 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. Like, fully ghosted. 👻
• --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. This one's mandatory in that case, no cap. 🚨
• --subst-mod, -s JC69|F81|HKY85|REV|SSREV|UNREST|R2|R2S|U2|U2S|R3|R3S|U3|U3S — (default REV). Nucleotide substitution model. Pick your fighter. ⚔️
• --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. Highkey we stay on HIGH. 👑
• --init-model, -M <mod_fname> — Initialize optimization procedure with specified tree model.
• --init-random, -r — Initialize parameters randomly. Chaos mode activated. 🎲
• --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. Row by row, she's methodical. 📋

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okay bestie that's literally the whole page, go forth and bootstrap responsibly 💜

and that's a wrap!! this was phyloBoot 1.4, dated May 2016 — thanks for reading my little manual rant, ily, bye 🫶🎀✨