phylogenetic.tree.fasttree: Construct and calibrate a phylogenetic tree from sequence...

In wdelva/RSimpactHelp: Pre- and Post-simulation helper functions for RSimpact Cyan

Description

Construct and calibrate a phylogenetic tree from sequence data

Usage

phylogenetic.tree.fasttree(dir.tree = dirfasttree, dir.seq = dirseqgen,
  fasttree.tool = "FastTree", calendar.dates = "dates.csv",
  simseqfile = "C.Epidemic.sequence.fasta", count.start = 1977,
  endsim = 40)

Arguments

dir.tree	Direcotry where we find the FastTree tool
dir.seq	Direcotry where we find sequences and sampling times files, it may be in the folder where simulation of sequences by sequence.simulation.seqgen() taken place
fasttree.tool	Name of the compiled file of FastTree
calendar.dates	File containing named sampling calendar times for each sequence
simseqfile	File containing sequences
count.start	Calendar year when the simulation started
endsim	Number of years when the simulation was done

Value

A time-stamped phylogenetic tree with annotation of internal nodes dates

wdelva/RSimpactHelp documentation built on Dec. 26, 2019, 3:42 a.m.