readLineages {dowser}

Read in all trees from a lineages file

Description

Read in all trees from a lineages file

Usage

readLineages(
  file,
  states = NULL,
  palette = NULL,
  run_id = "",
  quiet = TRUE,
  append = NULL,
  format = "nexus",
  type = "jointpars"
)

Arguments

file

IgPhyML lineage file

states

states in parsimony model

palette

deprecated

run_id

id used for IgPhyML run

quiet

avoid printing rubbish on screen?

append

string appended to fasta files

format

format of input file with trees

type

Read in parsimony reconstructions or ancestral sequence reconstructions? "jointpars" reads in parsimony states, others read in sequences in internal nodes

Value

A list of phylo objects from file.