ncdnj: Compute a Distance Matrix Using Normalized Compression...

In EnvNJ: Whole Genome Phylogenies Using Sequence Environments

Description

Computes a distance matrix using normalized compression distance.

Usage

ncdnj(wd)

Arguments

wd	character string indicating the path to the directory where the input files can be found (see details).

Details

The input files, which must be found at the wd provided, consist of a file named 'list.txt' containing the names of the fasta files to be analyzed (one per line). The referred fasta files also must be found at the provided wd. This function use zpaq to compress files. Thus, the zpaq software must be installed on your system and in the search path for executables if you wish to use this function.

Value

A list where the first element is a symmetric distance matrix and the second one is a phylogenetic tree build using NJ.

See Also

ncd()

Examples

try(ncdnj("./data_t"))

EnvNJ documentation built on Sept. 27, 2021, 5:07 p.m.