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Inputs/outputs in PHASE
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Running the programs
Contents
Using programs in the
PHASE
package
Subsections
Inputs/outputs in
PHASE
Data file format
File content
Pairing mask
Molecular sequences
Class section
Control file format
Tree file format
Substitution model parameters file format
Model parameters file content
Producing a model parameters file
Parameters displayed on the screen and output of each program
Clade file format
Control files
Structure of the control files
Datafile block
Model block
Simple substitution model
Mixed model for combined analyses of heterogeneous data
Using the programs in the
PHASE
package
likelihood
Using
likelihood
Control file for
likelihood
optimise
Using
optimise
Control file for
optimise
simulate
Using
simulate
Control file for
simulate
mlphase
Using
mlphase
Control file for
mlphase
mcmcphase
Using
mcmcphase
Using
consensus
Control file for
mcmcphase
PERTURBATION
block
PERTURBATION
Block for
MIXED
models
Proposals priority
analyser
Gowri-Shankar Vivek 2003-04-24
