Next:
Table of Contents
Contents
PHASE
: a Software Package for
Ph
ylogenetics
A
nd
S
equence
E
volution
Howsun J
OW
and Vivek G
OWRI-
S
HANKAR
Table of Contents
Introduction
Why is
PHASE
different from other phylogenetic programs?
Acknowledgements
How to read this manual ?
Aquiring and installing the software
MS-Windows installation
Unix-like system installation
Description of programs in the
PHASE
package
optimise
and
mlphase
mcmcphase
and
consensus
likelihood
simulate
analyser
Running the programs
Using programs in the
PHASE
package
Inputs/outputs in
PHASE
Data file format
Control file format
Tree file format
Substitution model parameters file format
Parameters displayed on the screen and output of each program
Clade file format
Control files
Structure of the control files
Datafile block
Model block
Using the programs in the
PHASE
package
likelihood
optimise
simulate
mlphase
mcmcphase
analyser
Elements of phylogenetic theory
Phylogenetic trees
Unrooted phylogenies
String representation of a tree
Branch lengths
Nucleotide substitution models
A Markov model of substitution
Transition matrices
Nucleotide substitution models implemented in
PHASE
Paired-site substitution models
RNA secondary structure
Theory of compensatory substitutions
Base-paired substitution models implemented in
PHASE
Refinements to substitution models
Invariant and discrete gamma models
The
MIXED
model
Bayesian phylogenetics
Bayes' theorem
Markov chain Monte-Carlo (MCMC)
Priors and proposals
Pitfalls of Markov chain Monte-Carlo techniques
Appendices
Some examples of control files
Control file for
likelihood
Control file for
optimise
Control file for
simulate
(1)
Control file for
simulate
(2)
Control file for
mlphase
(1)
Control file for
mlphase
(2)
Control file for
mcmcphase
(1)
Control file for
mcmcphase
(2)
Bibliography
About this document ...
Gowri-Shankar Vivek 2003-04-24
