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.

Author
Klaas Hartmann, Gavin Thomas, Arne Mooers, Jeffrey Joy, Walter Jetz
Date of publication
2013-09-11 15:23:31
Maintainer
Gavin Thomas <gavin.thomas@sheffield.ac.uk>
License
GPL (>= 3)
Version
0.1-2
URLs

View on CRAN

Man pages

accipitridaeBasicPastis
Accipitridae basic data
accipitridaeFullPastis
Accipitridae full data
conch
mrBayes output interrogator (COnstraint CHecker)
default_output_template
A sample output template for pastis_main and pastis_simple
pastis_data_1
Example data 1
pastis_data_2
Example data 2
pastis_data_3
Example data 3
pastis_data_3_trees
Example output
pastis_main
Phylogenetic Assembly with Soft Taxonomic Inferences
pastis-package
Phylogenetic Assembly with Soft Taxonomic Inferences.
pastis_simple
A simplified interface to the main pastis function.
read_input
Called by create_job to read input files

Files in this package

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