extended.tree.ex: An extension of an ape tree object which can be used to...

In PoonLab/clustuneR: Molecular clustering implementation and predictive optimization

An extension of an ape tree object which can be used to create clusters

Description

An extension of old.tree.ex maximum likelihood tree built using IQ-TREE with automatic model selection and 1000 parametric bootstraps. growth information and additional information useful for cluster identification were added by extend.tree.

Usage

extended.tree.ex

Format

A phylogenetic tree with 6 tips and 4 internal nodes. Node labels represent certainty. See ape's implementation of phylogenetic tree objects for information about tags within this object. In addition, there are 4 new objects created by functions within tree.setup.R

seq.info

See seq.info.ex, a data.table containing sequence meta data

node.info

Grouping of the meta.data present in seq.info assigned to various nodes in the tree, coupled with information important to clustering, such as mean divergence from root, or node certainty

path.info

Information regarding the path of edges from tips to the root of the tree. This is also necessary for some clustering algorithms, specifically step.cluster

growth.info

a data.table pairing new sequences, to a single node in the tree based on placements assigned by guppy and pplacer. The certainty of this placement, terminal branch length, neighbour, and branch length from new internal node to new neighbour are described

PoonLab/clustuneR documentation built on Jan. 29, 2024, 2:40 a.m.