BPP: Bayesian Phylogenetics and Phylogeography

Species Delimitation
Species Delimitation Mixing Parameters
Species Tree Inference
Species Tree Inference Mixing Parameters
Species and Starting Tree
Input Files


Output Files
Models

Locus-Specific Substitution Rates

Locus-Specific Heredity Scalars

Prior Distributions

Root Age

Theta

Locus-Specific Substitution Rates

Locus-Specific Heredity Scalars

Tree Topology

MCMC Specifications

Mixing Parameters


RNG Seed

(0 = seed from system clock)

MCMC Sampling

MCMC Output Files

Debugging Options
Control File
Warnings A map file, sequence file and Newick formatted starting tree must be specified.
Export Control File
Import Control File
Import Aligned Sequences
Export Aligned Sequences

Sequence Alignments

No sequence alignments have been attached for export to bpp sequence file.

Available Alignments for Population Labeling
Export Map File
Manage Population IDs
Population ID Sequences
Mapping of Sequence ID to Population ID
Sequence ID Population ID
Tree Viewer Canvas not supported
Import Trees
Run BPP

BPP Output

Summary of Posteriors

Plot Posterior Probabilities
Canvas not supported

Analysis of Convergence and Mixing

Not yet implemented.

Manuscript Preparation

Materials and Methods

Results

Literature Cited

Not yet implemented.

Supplemental Material

Not yet implemented.

Notebook
Data Provenance

Add note to data provenance file

Workspace
Working Directory

Color Schemes Sequence Dialog:
BPP Shell: