4.22. XMas: Robust estimation of genetic distances with information theory

XMas (jsa.phylo.xmas) is a tool to measure genetics distances between aligned sequences. It reads in a list of sequences from a fasta file format, and outputs a distance matrix in the format required by the PHYLIP package to run neighbour joining.

XMas is included in the Japsa package. Please see check the installation page for instructions.

4.22.1. Synopsis

jsa.phylo.xmas: Generate a distance matrix from aligned sequences

4.22.2. Usage

jsa.phylo.xmas [options]

4.22.3. Options

--input=s	Name of the input file, - for standard input (REQUIRED)
--output=s	Name of the file for output (distances in phylip format) (default=’output’)
--adapt	Use adaptive (default=’false’)
--help	Display this usage and exit (default=’false’)

4.22.4. Usage samples

At the moment, XMas is designed to worked with aligned sequences, with indels and wildcards (e.g., N) removed. XMas reads in these aligned sequences from a fasta file, and output the distances to a file in a format ready to run neibour-joining with PHYLIP. For examples:

jsa.phylo.xmas -i sequences.fas -o infile

And run phylip neighbor-joining from the distances in infile:

phylip neighbor