indelmiss: Insertion Deletion Analysis While Accounting for Possible Missing Data

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).

Version: 1.0.7
Depends: R (≥ 2.10)
Imports: Rcpp (≥ 0.11.2), ape (≥ 3.2), numDeriv (≥ 2012.9.1), phangorn (≥ 1.99.13)
LinkingTo: Rcpp
Suggests: testthat
Published: 2016-08-22
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang at binghamton.edu>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Citation: indelmiss citation info
Materials: NEWS
CRAN checks: indelmiss results

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Reference manual: indelmiss.pdf
Package source: indelmiss_1.0.7.tar.gz
Windows binaries: r-devel: indelmiss_1.0.7.zip, r-release: indelmiss_1.0.7.zip, r-oldrel: indelmiss_1.0.7.zip
OS X El Capitan binaries: r-release: indelmiss_1.0.7.tgz
OS X Mavericks binaries: r-oldrel: indelmiss_1.0.7.tgz

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