## ----eval=FALSE, warning=FALSE, message=FALSE---------------------------------
# # Load required packages
# library(alakazam)
# library(dowser)
# 
# # load example AIRR tsv data
# data(ExampleAirr)
# 
# # subset data for this example
# # only one clone used for speed, otherwise can include multiple clones
# ExampleAirr = ExampleAirr[ExampleAirr$clone_id %in% c("3170"),]
# 
# # Process example data into proper format, store isotype (optional)
# clones = formatClones(ExampleAirr, traits="c_call")
# 
# # Build maxmimum parsimony trees for first clone using
# # phangorn package in R
# trees <- getTrees(clones)
# 
# # simple tree plotting with ggtree R package with isotypes at tips
# plots <- plotTrees(trees, tips="c_call",tipsize=2)
# 
# # plot tree of largest clone
# plots[[1]]