pastis: Phylogenetic Assembly with Soft Taxonomic Inferences

A pre-processor for mrBayes that assimilates sequences, taxonomic information and tree constraints as per xxx. The main functions of interest for most users will be pastis_simple, pastis_main and conch. The main analysis is conducted with pastis_simple or pastis_main followed by a manual execution of mrBayes (>3.2). The placement of taxa not contained in the tree constraint can be investigated using conch.

Install the latest version of this package by entering the following in R:
install.packages("pastis")
AuthorKlaas Hartmann, Gavin Thomas, Arne Mooers, Jeffrey Joy, Walter Jetz
Date of publication2013-09-11 15:23:31
MaintainerGavin Thomas <gavin.thomas@sheffield.ac.uk>
LicenseGPL (>= 3)
Version0.1-2
http://cran.r-project.org/web/packages/pastis/

View on CRAN

Files

inst
inst/doc
inst/doc/pastis-vignette.rnw
inst/doc/pastis-vignette.pdf
NAMESPACE
data
data/accipitridaeBasicPastis.rda
data/pastis_data_2.rda
data/pastis_data_1.rda
data/pastis_data_3_trees.rda
data/pastis_data_3.rda
data/accipitridaeFullPastis.rda
R
R/pastis-package.R R/pastis.R
vignettes
vignettes/pastis-vignette.rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/accipitridaeBasicPastis.Rd man/accipitridaeFullPastis.Rd man/pastis_data_2.Rd man/read_input.Rd man/pastis_main.Rd man/pastis_simple.Rd man/pastis_data_3_trees.Rd man/conch.Rd man/pastis_data_1.Rd man/pastis_data_3.Rd man/default_output_template.Rd man/pastis-package.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.