The PAML web site has more information about obtaining the source code, installing the programs, and the background on how the analyses are run.
See the wrapper modules Bio::Tools::Run::Phylo::PAML::Baseml, Bio::Tools::Run::Phylo::PAML::Codeml, Bio::Tools::Run::Phylo::PAML::Yn00, and Bio::Tools::Run::Phylo::PAML::Evolver provide easy access for running batch sets of PAML analyses. The Bio::Tools::Phylo::PAML module can parse the output from these programs suitable for summarizing and parsing a batch of analyses.
With each version of PAML there appears to be changes to the output format so the BioPerl parser will often break. There isn't much we can do about this other than keep patching the parsing code. I think the current release (current being within 6 months of Feb 2006) has broken PAML parsing in BioPerl so we need someone to go in and fix/figure it out.
As of June 22, 2006, there is some experimental support for PAML 3.15 codeml and yn00 output; see this link (thanks to Jason) and this thread (thanks to Ryan) for details. At this moment there is incomplete support for PAML baseml output and will need more work before it operates properly with version 3.15 output.