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).

AuthorUtkarsh J. Dang and G. Brian Golding
Date of publication2016-08-22 01:59:09
MaintainerUtkarsh J. Dang <udang@binghamton.edu>
LicenseGPL (>= 2)
Version1.0.7

View on CRAN

Files

indelmiss
indelmiss/inst
indelmiss/inst/CITATION
indelmiss/tests
indelmiss/tests/testthat.R
indelmiss/tests/testthat
indelmiss/tests/testthat/test_main.R
indelmiss/src
indelmiss/src/RcppExports.cpp
indelmiss/src/loopC.cpp
indelmiss/NAMESPACE
indelmiss/NEWS
indelmiss/data
indelmiss/data/gardnerelladata.rda
indelmiss/data/mycobacteriumdata2.rda
indelmiss/data/mycobacteriumdata1.rda
indelmiss/R
indelmiss/R/indel-functions.R indelmiss/R/RcppExports.R
indelmiss/MD5
indelmiss/DESCRIPTION
indelmiss/man
indelmiss/man/plottree.Rd indelmiss/man/gardnerelladata.Rd indelmiss/man/plotp.Rd indelmiss/man/indelmiss-package.Rd indelmiss/man/mycobacteriumdata2.Rd indelmiss/man/mycobacteriumdata1.Rd indelmiss/man/plotrates.Rd indelmiss/man/indelrates.Rd indelmiss/man/plot.indelmiss.Rd indelmiss/man/print.indelmiss.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.