rbrothers: rbrothers: multiple change-point recombination detection

Share:

rbrothers is a phylogenetic recombination detection package. Starting with aligned DNA sequences, rbrothers uses the Bayesian multiple change-point model implemented in the JAVA package DualBrothers to create posterior tree probability plots. rbrothers automates the production of a reasonable set of candidate trees and provides trace plots and autocorrelation plots that allow the user to monitor the convergence and mixing of the Markov chain Monte Carlo algorithm.

Author
Vladimir Minin, Jan Irvahn
Date of publication
2015-07-31 19:02:46
Maintainer
Jan Irvahn <ji26@uw.edu>
License
GPL-3
Version
0.0-1

View on R-Forge

Man pages

breakpointCI
95% breakpoint credible interval
db
db
db.default
db.default
dualbrothers
Recombination Analysis via DualBrothers
epprofile
EPProfile
extractbasename
extract the basename from an rbrothers object
findbreakpoints
FindBreakPoints
plot.db
Plot a dualbrothers object
plotkappa
Plot Posterior values of Kappa for a DualBrothers object
plotmcmc
MCMC trace plot of log likelihoods
plotmu
Plot Posterior values of Mu for a DualBrothers object
plottree.db
Plots the most likely phylogenetic trees
readdb
import a dualbrothers object
summary.db
Summary of a dualbrothers object
topologyprofile
TopologyProfile

Files in this package

rbrothers/DESCRIPTION
rbrothers/NAMESPACE
rbrothers/R
rbrothers/R/breakpointCI.R
rbrothers/R/db.R
rbrothers/R/db.default.R
rbrothers/R/dualbrothers.R
rbrothers/R/epprofile.R
rbrothers/R/extractbasename.R
rbrothers/R/findbreakpoints.R
rbrothers/R/findmax.R
rbrothers/R/onLoad.R
rbrothers/R/plot.db.R
rbrothers/R/plotkappa.r
rbrothers/R/plotmcmc.r
rbrothers/R/plotmu.r
rbrothers/R/plottree.db.R
rbrothers/R/readdb.R
rbrothers/R/summary.db.R
rbrothers/R/topologyprofile.R
rbrothers/build
rbrothers/build/vignette.rds
rbrothers/demo
rbrothers/demo/00Index
rbrothers/demo/fimH_example.r
rbrothers/demo/salmonella_example.R
rbrothers/inst
rbrothers/inst/doc
rbrothers/inst/doc/rbrothers_tutorial.R
rbrothers/inst/doc/rbrothers_tutorial.Rnw
rbrothers/inst/doc/rbrothers_tutorial.pdf
rbrothers/inst/extdata
rbrothers/inst/extdata/KAL153
rbrothers/inst/extdata/KAL153/KAL153.cmdfile
rbrothers/inst/extdata/KAL153/KAL153.phy
rbrothers/inst/extdata/Primate
rbrothers/inst/extdata/Primate/primate.cmdfile
rbrothers/inst/extdata/Primate/primate.phy
rbrothers/inst/extdata/RW024
rbrothers/inst/extdata/RW024/RW024.cmdfile
rbrothers/inst/extdata/RW024/RW024.phy
rbrothers/inst/extdata/Salmonella
rbrothers/inst/extdata/Salmonella/Salmonella_fimA8.phy
rbrothers/inst/extdata/Salmonella/Salmonella_fimH8.phy
rbrothers/inst/extdata/UA0116
rbrothers/inst/extdata/UA0116/UA0116.cmdfile
rbrothers/inst/extdata/UA0116/UA0116.phy
rbrothers/inst/extdata/fimH
rbrothers/inst/extdata/fimH/fimH8.phy
rbrothers/inst/extdata/smalltrees
rbrothers/inst/extdata/smalltrees/five-input.tre
rbrothers/inst/extdata/smalltrees/four-input.tre
rbrothers/inst/extdata/smalltrees/six-input.tre
rbrothers/inst/extdata/smalltrees/three-input.tre
rbrothers/inst/java
rbrothers/inst/java/DualBrothers.jar
rbrothers/inst/java/colt.jar
rbrothers/man
rbrothers/man/breakpointCI.Rd
rbrothers/man/db.Rd
rbrothers/man/db.default.Rd
rbrothers/man/dualbrothers.Rd
rbrothers/man/epprofile.Rd
rbrothers/man/extractbasename.Rd
rbrothers/man/findbreakpoints.Rd
rbrothers/man/plot.db.Rd
rbrothers/man/plotkappa.Rd
rbrothers/man/plotmcmc.Rd
rbrothers/man/plotmu.Rd
rbrothers/man/plottree.db.Rd
rbrothers/man/readdb.Rd
rbrothers/man/summary.db.Rd
rbrothers/man/topologyprofile.Rd
rbrothers/vignettes
rbrothers/vignettes/rbrothers_tutorial.Rnw