BPP: Bayesian Phylogenetics and Phylogeograpy

Configuration
Control File
Sequence Data
Map File
Trees
Run BPP
Results
Notebook
Preferences

Species Delimitation

Species Delimitation Mixing Parameters

Species Tree Inference

Species Tree Inference Mixing Parameters

Species and Starting Tree

Input Files Individual to population map file:
Sequence data file:
Remove sites with ambiguity data

Output Files MCMC tree output file:
Results output file:

Models

Locus-Specific Substitution Rates

Locus-Specific Heredity Scalars

Prior Distributions

Root Age

Mean: Variance: Dirichlet (alpha):

Theta

Mean: Variance:

Locus-Specific Substitution Rates

Dirichlet (alpha):

Locus-Specific Heredity Scalars

Mean: Variance:

Tree Topology

MCMC Specifications

Mixing Parameters

Auto-tuning of mixing parameters
GBtj: GBspr: theta: tau: mix: locusrate: seqerr:

RNG Seed

(0 = seed from system clock)

MCMC Sampling

Burn-in: Replicates: Sampling:

MCMC Output Files

Species trees Gene trees Locus rates Heredity scalars

Debugging Options Likelihood On (uncheck to sample from priors using no data)

Control File

Warnings A map file, sequence file and Newick formatted starting tree must be specified.

Export Control File Save Control File:

Import Control File Open Control File:

Import Aligned Sequences Sequence Data File:

Export Aligned Sequences Sequence File Name: Choose Map File:

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 Enter name of population:

Population ID	Sequences

Mapping of Sequence ID to Population ID

Sequence ID	Population ID

Tree Viewer

Import Trees Tree File: Relative Scaling Cladogram

Run BPP Select BPP Control File:

BPP Output

        BPPg version 0.2.0 Bruce Rannala, UC Davis

Summary of Posteriors

Plot Posterior Probabilities Open Output File:

Analysis of Convergence and Mixing

Not yet implemented.

Manuscript Preparation

Select BPP Control File:

Materials and Methods

Results

   Not yet implemented.

Literature Cited

Not yet implemented.

Supplemental Material

Not yet implemented.

Notebook

Data Provenance

Save File As:

Add note to data provenance file

Workspace

Working Directory

Color Schemes Sequence Dialog: BPP Shell:

BPP: Bayesian Phylogenetics and Phylogeography

Locus-Specific Substitution Rates

Locus-Specific Heredity Scalars

Root Age

Theta

Locus-Specific Substitution Rates

Locus-Specific Heredity Scalars

Tree Topology

Mixing Parameters

RNG Seed

MCMC Sampling

MCMC Output Files

Sequence Alignments

BPP Output

Summary of Posteriors

Analysis of Convergence and Mixing

Manuscript Preparation

Materials and Methods

Results

Literature Cited

Supplemental Material