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).
|Depends:||R (≥ 2.10)|
|Imports:||Rcpp (≥ 0.11.2), ape (≥ 3.2), numDeriv (≥ 2012.9.1), phangorn (≥ 1.99.13)|
|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)]|
|Citation:||indelmiss citation info|
|CRAN checks:||indelmiss results|
|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 Mavericks binaries:||r-release: indelmiss_1.0.7.tgz, r-oldrel: indelmiss_1.0.7.tgz|
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