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pastis (version 0.1-2)

Phylogenetic Assembly with Soft Taxonomic Inferences

Description

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.

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Version

Install

install.packages('pastis')

Monthly Downloads

38

Version

0.1-2

License

GPL (>= 3)

Maintainer

Last Published

September 11th, 2013

Functions in pastis (0.1-2)

conch

mrBayes output interrogator (COnstraint CHecker)
pastis_data_1

Example data 1
pastis_data_3_trees

Example output
pastis_main

Phylogenetic Assembly with Soft Taxonomic Inferences
accipitridaeFullPastis

Accipitridae full data
pastis_data_3

Example data 3
default_output_template

A sample output template for pastis_main and pastis_simple
pastis-package

Phylogenetic Assembly with Soft Taxonomic Inferences.
read_input

Called by create_job to read input files
pastis_data_2

Example data 2
accipitridaeBasicPastis

Accipitridae basic data
pastis_simple

A simplified interface to the main pastis function.