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/paml4.5/README.txt

README.txt for PAML

PAML (for Phylogentic Analysis by Maximum Likelihood) contains a few
programs for model fitting and phylogenetic tree reconstruction using
nucleotide or amino-acid sequence data.  ANSI C source codes as well
as Win32 and MC OSX excutables are distributed.  Win32 executables are 
in the folder bin.  Type, say, 
	bin\codeml
to run the codeml program.  For UNIX and OS-X s
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/paml4.5/examples/DatingSoftBound/readme.txt

MCMCTREE
Ziheng Yang

4 October 2005, modified in March 2007 & August 2009

(A) You can use the files in this folder to run mcmctree to duplicate the
results of Yang and Rannala (2006: table 3) and Rannala and Yang
(2007, table table 2).  

    ..\..\bin\mcmctree

Make your window wider (100 columns) before running the program.  See
the section on mcmctree in the paml manual for a desc
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/paml4.5/examples/HIVNSsites/README.txt

Notes by Ziheng Yang
Last modified 16 May 2003

This folder contains example data files for the HIV-1 env V3 region
analyzed in Yang et al. (2000).  This is the 10th data set analyzed
and the results are in table 12 in that paper.  The default
specification in the control file codeml.ctl

      NSsites = 0 1 2

will fit the onw-ratio model (M0), neutral (M0) and selection (M2)
models.  
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/paml4.5/examples/MHC.Swanson2002MBE/README.txt

Notes by Ziheng Yang
Last modified: 25 March 2009

(A) This is the MHC dataset analyzed by Yang &
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/paml4.5/examples/MouseLemurs/README.txt

README.txt
Ziheng Yang, 27 January 2003


This folder contains files for the local-clock likelih
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/paml4.5/examples/MouseLemurs/README2.txt

README.txt
Ziheng Yang, January 2004

(A)  Overview

This folder includes the files used in Yan
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/paml4.5/examples/README.txt

Readme.txt

Updated November 2001

This folder contains a few files as well as sub folders with 
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/paml4.5/examples/TipDate/README.txt

README.txt
18 September 2011, Ziheng Yang

This example data file is for duplicating the analysis
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