convert_XML: Create BEAST XML file

In JoelJWilson/BEAUtiXMLconvert: Edit XML files produced by BEAUti

Description

Imports sequences from a file and places them in an XML file generated by BEAUti for use with BEAST.

Usage

convert_XML(input, datatype, template, file, dates = NULL, location = NULL,
  chainLength = NULL, storeEvery = NULL)

Arguments

input	The name of the input file containing the alignment. Works with .nex, .fasta and .phy files
datatype	The type of data used in the alignment input file. Either 'nucleotide', 'aminoacid', or 'binary'.
template	The name of the BEAST input XML file to be used as a template. This file can be produced by BEAUti
file	The name of the file that the resulting XML file will be written to.
dates	The name of the tab delimited file containing tip date data.
location	The name of the tab delimited file containing location data.
chainLength	An integer determining the length of the MCMC chain. If not stated will stay as the value specified in the original template XML file.
storeEvery	An integer determining how often to store the state. If not stated will stay as the value specified in the original template XML file.

JoelJWilson/BEAUtiXMLconvert documentation built on May 30, 2019, 6:12 a.m.