mycobacteriumdata1

Gene family memberships and a phylogenetic tree for ten species from the genus Mycobacterium.

datasets

Genome-wide gene insertion and deletion rates can be modelled in a maximum
likelihood framework with the additional flexibility of modelling potential missing
data using the models included within. These models simultaneously estimate insertion
and deletion (indel) rates of gene families and proportions of "missing" data for
(multiple) taxa of interest. The likelihood framework is utilized for parameter
estimation. A phylogenetic tree of the taxa and gene presence/absence patterns
(with data ordered by the tips of the tree) are required. See Dang et al.
(2016) <doi:10.1534/genetics.116.191973> for more details.

Utkarsh Dang

indelmiss

Insertion Deletion Analysis While Accounting for Possible
Missing Data

mycobacteriumdata1 function

Contains a list that comprises a tree (called "tree") and phyletic gene family membership data (called "phyl") as its components. The tree is in the ape package phylo format. The data component consists of a data frame of 0/1 patterns with the different patterns as the rows and the 10 taxa as the columns. An entry of 1 (0) describe gene presence (absence) in the taxa.

mycobacteriumdata1: Mycobacterium data phyletic data (gene family memberships) and tree

Description

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Examples