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**************************************
Evolutionary analysis using likelihood
**************************************
Specifying substitution models
==============================
Canned models
-------------
*To be written.*
MotifChange and predicates
--------------------------
*To be written.*
Rate heterogeneity models
-------------------------
*To be written.*
Specifying likelihood functions
===============================
Scoping parameters on trees
---------------------------
*To be written.*
Specifying parameter values
---------------------------
*To be written.*
.. constant, bounds, initial
Specifying rate heterogeneity functions
---------------------------------------
*To be written.*
Specifying Phylo-HMMs
---------------------
*To be written.*
Fitting likelihood functions
============================
Choice of optimisers
--------------------
*To be written.*
Checkpointing runs
------------------
*To be written.*
How to check your optimisation was successful.
----------------------------------------------
*To be written.*
.. Try again, use global optimisation, check maximum numbers of calculations not exceeded.
Getting statistics out of likelihood functions
==============================================
*To be written.*
.. the annotated tree, the tables, getParamValue
Testing hypotheses
==================
*To be written.*
.. LRTs, assuming chisq, bootstrapping, randomisation
Determining confidence intervals on MLEs
========================================
*To be written.*
Saving results
==============
*To be written.*
Visualising statistics on trees
===============================
*To be written.*
Reconstructing ancestral sequences
==================================
*To be written.*
.. most likely ancestors, the complete posterior probabilities
Tips for improved performance
=============================
*To be written.*
Sequentially build the fitting
------------------------------
*To be written.*
.. start with null, then modify lf to alternate. Don't forget to record the values you need.
.. how to specify the alt so it is the null for rate heterogeneity models
Sampling
--------
*To be written.*
.. using a subset of data
|
