phylogenetic.tree.fasttree.par: Construct phylogenetic tree with FastTree and calibrate same...

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

Description

Construct phylogenetic tree with FastTree and calibrate same tree with treedater from sequence alignment

Usage

phylogenetic.tree.fasttree.par(dir.tree = dirfasttree,
  sub.dir.rename = sub.dir.rename, fasttree.tool = "FastTree",
  calendar.dates = "samplingtimes.all.csv",
  simseqfile = "C.Epidemic_seed.seq.bis.sim.nwk.fasta", count.start = 1977,
  endsim = 40, clust = TRUE)

Arguments

dir.tree	Direcotry where we find the FastTree tool
sub.dir.rename	sub directory where we find sequences and sampling times files and where the simulation outputs will be stored
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
clust	Logic parameter TRUE when running simulation on cluster and FALSE on personal computer

Value

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

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