R: Maximum-Likelihood Perfect Phylogeny Inference at Scale

# Maximum-Likelihood Perfect Phylogeny Inference at Scale

## Documentation for package ‘scistreer’ version 1.2.1

- DESCRIPTION file
- Package README

## Help Pages

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