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
    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
    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.
    PLoS One, 6, e17244/pp. 1-22, 2011.
    Full text (pdf) | errata (pdf)
    Supporting Information: text_s1.pdf | data_s1.txt