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. For more details, see Utkarsh J. Dang, Alison M. Devault, Tatum D. Mortimer, Caitlin S. Pepperell, Hendrik N. Poinar, G. Brian Golding (2016). Gene insertion deletion analysis while accounting for possible missing data. Genetics (accepted).

Documentation

Manual: indelmiss.pdf
Vignette: None available.

Maintainer: Utkarsh J. Dang <udang at binghamton.edu>

Author(s): Utkarsh J. Dang and G. Brian Golding

Install package and any missing dependencies by running this line in your R console:

install.packages("indelmiss")

Depends R (>= 2.10)
Imports Rcpp(>=0.11.2), ape(>=3.2), numDeriv(>=2012.9.1), phangorn(>=1.99.13)
Suggests testthat
Enhances
Linking to Rcpp
Reverse
depends
Reverse
imports
Reverse
suggests
Reverse
enhances
Reverse
linking to

Package indelmiss
Materials
URL
Task Views
Version 1.0.7
Published 2016-08-22
License GPL (>= 2)
BugReports
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks indelmiss check results
Package source indelmiss_1.0.7.tar.gz