Readme.txt

Updated November 2001

This folder contains a few files as well as sub folders with sequence
data files, tree files, and control files that have been used in my
papers which describe methods implemented in programs distributed in
the package.  Unfortunately paml programs are getting large and with
100% probability contain bugs.  Options/models we used before were
tested extensively at the time the paper was published but might have
been broken later on.  So my advice is that you use the example data
sets to duplicate our results, (1) to make sure that the programs are
working, and (2) to get familiar with the format specifications and
interpretations.

The list below is imcomplete.  You should see the readme files in the
sub folders to know what examples are included and for the references.

dndstestG1.nuc: data from Yang & Nielsen (1998) for ds and dn estimation 
hummt25.nuc   : humuman mt data used in Yang & Kumar (1996) for pamp 
mtprim9.nuc   : mt DNA for 9 species. I can't remember what they are for. 
abglobin.aa   : alpha and beta globin genes, old data set
abglobin.nuc  : alpha and beta globin protein sequences.
YN00abglobin.result: results of pairwise estimation of ds and dn from abglobin.nuc, using yn00 and ml (codeml)
clock         : folder containing files for clock dating (Yoder & Yang 2000) and Rambaut's tip date models (the exampleTipDate files)
HIVNSsites    : The HIV env data set for NSsites models, used in Yang Nielsen Goldman &Pedersen (2000)  
lysozyme      : The "small" and "large" lysozyme data sets for testing slection along lineages (Yang 1998) and for the branch-site models (Yang & Nielsen 2002)
lysin         : The lysin data set for NSsites models (used in Yang, Swanson & Vaquier 2000), with results for the posterior probability plot