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.

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 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

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

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