Function reference • LakshmanTutorials

Building Trees

Functions for building phylogenetic trees

hclust() plot(<hclust>): Hierarchical Clustering (from stats)

DistanceMatrix(): Calculate the Distances Between Sequences (from DECIPHER)

TreeLine(): Construct a Phylogenetic Tree (from DECIPHER)

as.dendrogram() as.hclust(<dendrogram>) plot(<dendrogram>) cut(<dendrogram>) merge(<dendrogram>) nobs(<dendrogram>) print(<dendrogram>) rev(<dendrogram>) str(<dendrogram>) is.leaf(): General Tree Structures (from stats)

WriteDendrogram(): Write a Dendrogram to Newick Format (from DECIPHER)

Comparing Trees

Functions for comparing phylogenetic trees

readBStringSet() readDNAStringSet() readRNAStringSet() readAAStringSet() fasta.seqlengths() fasta.index() fastq.seqlengths() fastq.geometry() writeXStringSet() saveXStringSet(): Read/write an XStringSet object from/to a file (from Biostrings)

dist.topo(): Topological Distances Between Two Trees (from ape)