indelmiss: Insertion Deletion Analysis While Accounting for Possible Missing Data

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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).

Author
Utkarsh J. Dang and G. Brian Golding
Date of publication
2016-08-22 01:59:09
Maintainer
Utkarsh J. Dang <udang@binghamton.edu>
License
GPL (>= 2)
Version
1.0.7

View on CRAN

Man pages

gardnerelladata
Gardnerella vaginalis phyletic data (gene family memberships)...
indelmiss-package
Insertion deletion analysis while accounting for possible...
indelrates
Function for estimating indel rates while accounting for...
mycobacteriumdata1
Mycobacterium data phyletic data (gene family memberships)...
mycobacteriumdata2
Alternate Mycobacterium tree.
plot.indelmiss
Plot parameter estimates from the model fit
plotp
Plot estimates for the parameter that accounts for possible...
plotrates
Plot estimates for insertion and deletion rates
plottree
Plot the tree used the branches colored according to the...
print.indelmiss
Print summary information from fit

Files in this package

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