Maximum-Likelihood Perfect Phylogeny Inference at Scale

Documentation for package ‘scistreer’ version 1.2.0

annotate_tree	Find maximum lilkelihood assignment of mutations on a tree
get_mut_graph	Convert a single-cell phylogeny with mutation placements into a mutation graph
gtree_small	Smaller example annotated tree built from P_small
ladderize	From ape; will remove once new ape version is released https://github.com/emmanuelparadis/ape/issues/54
mut_nodes_small	Mutation placements calculated from tree_small and P_small
mut_to_tree	Transfer mutation assignment onto a single-cell phylogeny
perform_nni	Maximum likelihood tree search via NNI
plot_phylo_heatmap	Plot phylogeny and mutation heatmap
P_example	Example genotype probability matrix
P_small	Smaller example genotype probability matrix
run_scistree	Run the scistree workflow
score_tree	Score a tree based on maximum likelihood
to_phylo	Convert the phylogeny from tidygraph to phylo object modified from R package alakazam, converts a tbl_graph to a phylo object
tree_small	Smaller example tree built from P_small
tree_upgma	Example tree built using UPGMA from P_small