Subcommand: random placements - lczech/gappa GitHub Wiki

Create a set of random phylogenetic placements on a given reference tree.

Usage: gappa simulate random-placements [options]

Input
--reference-tree	Required. TEXT File containing a reference tree in newick format.
--pquery-count	Required. UINT=0 Number of pqueries to create.
--subtree	INT=-1 If given, only generate random placements in one of the subtrees of the root node. For example, if the root is a trifurcation, values 0-2 are allowed.
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 set of random phylogenetic placmeents on a given reference tree. It generates as many pqueries as given by --pquery-count, named pquery_n, with each having a random number of placements on nearby branches of a randomly chosen edge.

The output file is named random-placements.jplace, 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