References for the original Phyml package

1. S. Guindon AND O. Gascuel
   A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihoods
   Systematic Biology 52(5):696-704, 2003.
   
   Original manual in the phyml package (phyml-20100824)

References for the modified version

1. Miyazawa, Sanzo
   Prediction of contact residue pairs based on co-substitution between sites in protein structures
   doi:10.1371/journal.pone.0054252
   PLoS One, 8, e54252/pp. 1-20, 2013.
   Full text (pdf)
   Supporting Information: Figures S1-S6 and Table S1 (tar bz2 file) | Data S1 (tar bz2 file)


2. Miyazawa, Sanzo
   Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences
   doi:10.1371/journal.pone.0028892
   PLoS One, 6, e28892/pp. 1-20, 2011.
   Full text (pdf)


3. Miyazawa, Sanzo
   Selective constraints on amino acids estimated by a mechanistic codon substitution model with multiple nucleotide changes.
   doi:10.1371/journal.pone.0017244
   PLoS One, 6, e17244/pp. 1-22, 2011.
   Full text (pdf) | errata (pdf)
   Supporting Information: text_s1.pdf | data_s1.txt