PAUP* FAQ: Questions

Last updated 22 February 2007
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Questions about the PAUP* FAQ

General questions

Setting the optimality criterion:

Importing non-NEXUS file formats:

Deleting and restoring taxa, excluding and including characters (sites):

Combing data sets

Creating data partitions:

Defining and using topological constraints:

Tree files:

Questions about searching

Questions about PAUP* interfaces

The Macintosh Interface

The DOS Interface

The Windows Interface

Questions about parsimony

Parsimony-based tests

Weighting Characters

Goodness-of-fit Statistics

Questions about likelihood

Selecting substitution models

Likelihood scores

Transition/transversion ratio

Rate heterogeneity

Ancestral States

Questions about distance

Examples of paup blocks for conducting entire analyses