Subcommand: krd

Calcualte the pairwise Kantorovich-Rubinstein (KR) distance matrix between samples.

Usage: gappa analyze krd [options]

Options

Input
--jplace-path	Required. TEXT ... List of jplace files or directories to process. For directories, only files with the extension .jplace are processed.
Settings
--exponent	FLOAT=1 Exponent for KR integration.
--normalize	Divide the KR distance by the tree length to get normalized values.
--point-mass	Treat every pquery as a point mass concentrated on the highest-weight placement.
--ignore-multiplicities	Set the multiplicity of each pquery to 1.
Matrix Output
--out-dir	TEXT=. Directory to write files to
--file-prefix	TEXT File prefix for output files
--matrix-format	TEXT in {list,matrix,triangular}=matrix Format of the output matrix file.
--omit-matrix-labels	If set, the output matrix is written without column and row labels.

Description

Calculates the Kantorovich-Rubinstein distance between a collection of jplace samples. The command is a re-implementation of guppy kr, see there for more details.

Details

The command reads in the jplace samples and calculates their pairwise KR distances. The result is printed to a symmetrical matrix by default, but can also be printed as a list or an upper triangular matrix.

Citation

More information on the method can be found in

Evans SN, Matsen FA (2012), "The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples.", J. R. Stat. Soc. Ser. B Stat. Methodol., vol. 74, pp. 569–592, doi:10.1111/j.1467-9868.2011.01018.x