rbrothers: rbrothers: multiple change-point recombination detection

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.

AuthorVladimir Minin, Jan Irvahn
Date of publication2015-07-31 19:02:46
MaintainerJan Irvahn <ji26@uw.edu>
LicenseGPL-3
Version0.0-1

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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

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

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