readLineages: Read in all trees from a lineages file
In dowser: B Cell Receptor Phylogenetics Toolkit

View source: R/TreeFunctions.R

readLineages

R Documentation

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.

dowser documentation built on May 29, 2024, 3:06 a.m.

dowser index

Package overview README.md Building trees with paired heavy and light chain data Build Lineage Trees Discrete Trait Analysis Measurable evolution Plotting Lineage Trees Quickstart Reconstruct Clonal Germlines Reconstruct Intermediate Sequences Build B cell lineage trees Building trees with paired heavy and light chain data Detect ongoing B cell evolution Discrete trait analysis Dowser: Simple lineage tree construction Plot B cell lineage trees Reconstruct clonal germline sequences Reconstruct intermediate sequences

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