This is makeindex, version 2.15 [TeX Live 2012] (kpathsea + Thai support).
Scanning input file phyml-manual.idx....done (117 entries accepted, 0 rejected).
Sorting entries....done (826 comparisons).
Generating output file phyml-manual.ind....done (162 lines written, 0 warnings).
Output written in phyml-manual.ind.
Transcript written in phyml-manual.ilg.