Subcommand: random tree - lczech/gappa GitHub Wiki

Create a random tree with a given numer of leaf nodes.

Usage: gappa simulate random-tree [options]

Input
--leaf-count	Required. UINT=0 Number of leaf nodes (taxa) to create.
Output
--out-dir	TEXT=. Directory to write output files to.
--file-prefix	TEXT File prefix for output files. Most gappa commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.
--file-suffix	TEXT File suffix for output files. Most gappa commands use the command name as the base name for file output. This option amends the base name, to distinguish runs with different data.
--compress	FLAG If set, compress the output files using gzip. Output file extensions are automatically extended by .gz.
Global Options
--allow-file-overwriting	FLAG Allow to overwrite existing output files instead of aborting the command.
--verbose	FLAG Produce more verbose output.
--threads	UINT Number of threads to use for calculations.
--log-file	TEXT Write all output to a log file, in addition to standard output to the terminal.

The command creates a random tree with a given number of leaf nodes (taxa). The taxa are named with simple letter combinations, going a, ..., z, aa, ..., az, ba, ..., and are randomly distributed over the tree. The branch lengths are randomly chosen in the unit interval.

The output file is random-tree.newick, potentially using the --file-prefix and --file-suffix if provided.

When using this method, please do not forget to cite

Lucas Czech, Pierre Barbera, Alexandros Stamatakis. Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data. Bioinformatics, 2020. doi:10.1093/bioinformatics/btaa070