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 Phylogenetic Analysis by Maximum Likelihood (PAML)
 
-PAML is a program package for phylogenetic analyses of DNA or protein
-sequences using maximum likelihood, and is maintained and distributed
-by Ziheng Yang.
-
-Possible uses of the programs are:
-- Estimation of branch lengths in a phylogenetic tree and parameters
-  in the evolutionary model such as the transition/transversion rate
-  ratio, the shape parameter of the gamma distribution for variable
-  evolutionary rates among sites, and rate parameters for different
-  genes;
-- Test of hypotheses concerning sequence evolution, such as rate
-  constancy and independence among nucleotide or amino acid sites, rate
-  constancy among lineages (the molecular clock), and homogeneity of
-  evolutionary process in multiple genes;
-- Calculation of substitution rates at sites;
-- Reconstruction of ancestral nucleotide or amino acid sequences;
-- Simulation of nucleotide, codon, and amino acid sequence data sets;
-- Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods.
+PAML is a package of programs for phylogenetic analyses of DNA or protein
+sequences using maximum likelihood.  It is not good for tree making.  It may be
+used to estimate parameters and test hypotheses for the study the evolutionary
+process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY,
+PhyML, or RaxML.
 
 WWW: http://abacus.gene.ucl.ac.uk/software/paml.html