\BOOKMARK [1][-]{section.1}{Availability}{}% 1
\BOOKMARK [1][-]{section.2}{Authors}{}% 2
\BOOKMARK [1][-]{section.3}{Overview}{}% 3
\BOOKMARK [1][-]{section.4}{Bug report}{}% 4
\BOOKMARK [1][-]{section.5}{Installing PhyML}{}% 5
\BOOKMARK [2][-]{subsection.5.1}{Sources and compilation}{section.5}% 6
\BOOKMARK [2][-]{subsection.5.2}{Installing PhyML on UNIX-like systems \(including Mac OS\)}{section.5}% 7
\BOOKMARK [2][-]{subsection.5.3}{Installing PhyML on Microsoft Windows}{section.5}% 8
\BOOKMARK [2][-]{subsection.5.4}{Installing the parallel version of PhyML}{section.5}% 9
\BOOKMARK [1][-]{section.6}{Program usage.}{}% 10
\BOOKMARK [2][-]{subsection.6.1}{PHYLIP-like interface}{section.6}% 11
\BOOKMARK [3][-]{subsubsection.6.1.1}{Input Data sub-menu}{subsection.6.1}% 12
\BOOKMARK [3][-]{subsubsection.6.1.2}{Substitution model sub-menu}{subsection.6.1}% 13
\BOOKMARK [3][-]{subsubsection.6.1.3}{Tree searching sub-menu}{subsection.6.1}% 14
\BOOKMARK [3][-]{subsubsection.6.1.4}{Branch support sub-menu}{subsection.6.1}% 15
\BOOKMARK [2][-]{subsection.6.2}{Command-line interface}{section.6}% 16
\BOOKMARK [2][-]{subsection.6.3}{XML interface}{section.6}% 17
\BOOKMARK [2][-]{subsection.6.4}{Parallel bootstrap}{section.6}% 18
\BOOKMARK [1][-]{section.7}{Inputs \046 outputs for command-line and PHYLIP interface }{}% 19
\BOOKMARK [2][-]{subsection.7.1}{Sequence formats}{section.7}% 20
\BOOKMARK [3][-]{subsubsection.7.1.1}{Gaps and ambiguous characters}{subsection.7.1}% 21
\BOOKMARK [3][-]{subsubsection.7.1.2}{Specifying outgroup sequences}{subsection.7.1}% 22
\BOOKMARK [2][-]{subsection.7.2}{Tree format}{section.7}% 23
\BOOKMARK [2][-]{subsection.7.3}{Multiple alignments and trees}{section.7}% 24
\BOOKMARK [2][-]{subsection.7.4}{Custom amino-acid rate model}{section.7}% 25
\BOOKMARK [2][-]{subsection.7.5}{Topological constraint file}{section.7}% 26
\BOOKMARK [2][-]{subsection.7.6}{Output files}{section.7}% 27
\BOOKMARK [2][-]{subsection.7.7}{Treatment of invariable sites with fixed branch lengths}{section.7}% 28
\BOOKMARK [1][-]{section.8}{Inputs \046 outputs for the XML interface }{}% 29
\BOOKMARK [2][-]{subsection.8.1}{Mixture models in PhyML}{section.8}% 30
\BOOKMARK [2][-]{subsection.8.2}{Partitions}{section.8}% 31
\BOOKMARK [2][-]{subsection.8.3}{Combining mixture and partitions in PhyML: the theory}{section.8}% 32
\BOOKMARK [2][-]{subsection.8.4}{The XML format and its use in PhyML}{section.8}% 33
\BOOKMARK [2][-]{subsection.8.5}{Setting up mixture and partition models in PhyML: the basics}{section.8}% 34
\BOOKMARK [2][-]{subsection.8.6}{XML options}{section.8}% 35
\BOOKMARK [3][-]{subsubsection.8.6.1}{phyml component}{subsection.8.6}% 36
\BOOKMARK [3][-]{subsubsection.8.6.2}{topology component}{subsection.8.6}% 37
\BOOKMARK [3][-]{subsubsection.8.6.3}{ratematrices component}{subsection.8.6}% 38
\BOOKMARK [3][-]{subsubsection.8.6.4}{equfreqs component}{subsection.8.6}% 39
\BOOKMARK [3][-]{subsubsection.8.6.5}{branchlengths component}{subsection.8.6}% 40
\BOOKMARK [3][-]{subsubsection.8.6.6}{siterates component}{subsection.8.6}% 41
\BOOKMARK [3][-]{subsubsection.8.6.7}{partitionelem and mixtureelem components}{subsection.8.6}% 42
\BOOKMARK [2][-]{subsection.8.7}{A simple example: GTR + 4 + I}{section.8}% 43
\BOOKMARK [2][-]{subsection.8.8}{A second example: LG4X}{section.8}% 44
\BOOKMARK [2][-]{subsection.8.9}{An example with multiple partition elements}{section.8}% 45
\BOOKMARK [2][-]{subsection.8.10}{Branch lengths with invariants and partionned data}{section.8}% 46
\BOOKMARK [1][-]{section.9}{Citing PhyML}{}% 47
\BOOKMARK [1][-]{section.10}{Other programs in the PhyML package}{}% 48
\BOOKMARK [2][-]{subsection.10.1}{PhyTime}{section.10}% 49
\BOOKMARK [3][-]{subsubsection.10.1.1}{Installing PhyTime}{subsection.10.1}% 50
\BOOKMARK [3][-]{subsubsection.10.1.2}{Running PhyTime}{subsection.10.1}% 51
\BOOKMARK [3][-]{subsubsection.10.1.3}{Upper bounds of model parameters}{subsection.10.1}% 52
\BOOKMARK [3][-]{subsubsection.10.1.4}{PhyTime specific options}{subsection.10.1}% 53
\BOOKMARK [3][-]{subsubsection.10.1.5}{PhyTime output}{subsection.10.1}% 54
\BOOKMARK [3][-]{subsubsection.10.1.6}{ClockRate vs. EvolRate}{subsection.10.1}% 55
\BOOKMARK [3][-]{subsubsection.10.1.7}{Effective sample size}{subsection.10.1}% 56
\BOOKMARK [3][-]{subsubsection.10.1.8}{Prior distributions of model parameters}{subsection.10.1}% 57
\BOOKMARK [3][-]{subsubsection.10.1.9}{Citing PhyTime}{subsection.10.1}% 58
\BOOKMARK [1][-]{section.11}{Recommendations on program usage}{}% 59
\BOOKMARK [2][-]{subsection.11.1}{PhyML}{section.11}% 60
\BOOKMARK [2][-]{subsection.11.2}{PhyTime}{section.11}% 61
\BOOKMARK [1][-]{section.12}{Frequently asked questions}{}% 62
\BOOKMARK [1][-]{section.13}{Acknowledgements}{}% 63