\indexentry{RAxML|hyperpage}{5}
\indexentry{GARLI|hyperpage}{5}
\indexentry{bug|hyperpage}{5}
\indexentry{compilation|hyperpage}{5}
\indexentry{MPI|hyperpage}{6}
\indexentry{bootstrap!parallel|hyperpage}{6}
\indexentry{run ID|hyperpage}{8}
\indexentry{$\kappa$|hyperpage}{10}
\indexentry{ts/tv ratio|hyperpage}{10}
\indexentry{PAML|hyperpage}{10}
\indexentry{PHYLIP|hyperpage}{10}
\indexentry{invariable sites|hyperpage}{10}
\indexentry{proportion of invariants|hyperpage}{10}
\indexentry{gamma distribution (discrete)!mean vs. median|hyperpage}{10}
\indexentry{gamma distribution (discrete)!number of categories|hyperpage}{10}
\indexentry{gamma distribution (discrete)!shape parameter|hyperpage}{10}
\indexentry{BioNJ|hyperpage}{12}
\indexentry{command-line options!\x{--input}|hyperpage}{13}
\indexentry{command-line options!\x{--data\_type}|hyperpage}{13}
\indexentry{sequence format!interleaved|hyperpage}{13}
\indexentry{sequence format!sequential|hyperpage}{13}
\indexentry{command-line options!\x{--sequential}|hyperpage}{13}
\indexentry{multiple data sets|hyperpage}{14}
\indexentry{command-line options!\x{--multiple}|hyperpage}{14}
\indexentry{command-line options!\x{--pars}|hyperpage}{14}
\indexentry{bootstrap|hyperpage}{14}
\indexentry{command-line options!\x{--bootstrap}|hyperpage}{14}
\indexentry{substitution models!DNA|hyperpage}{14}
\indexentry{substitution models!amino acids|hyperpage}{14}
\indexentry{command-line options!\x{--model}|hyperpage}{14}
\indexentry{custom models|hyperpage}{15}
\indexentry{command-line options!\x{--aa\_rate\_file}|hyperpage}{15}
\indexentry{frequencies!nucleotide|hyperpage}{15}
\indexentry{frequencies!amino-acid|hyperpage}{15}
\indexentry{stationary frequencies|hyperpage}{15}
\indexentry{command-line options!\x{-f}|hyperpage}{15}
\indexentry{$\kappa$|hyperpage}{16}
\indexentry{ts/tv ratio|hyperpage}{16}
\indexentry{command-line options!\x{--ts/tv}|hyperpage}{16}
\indexentry{proportion of invariants|hyperpage}{16}
\indexentry{invariable sites|hyperpage}{16}
\indexentry{command-line options!\x{--pinv}|hyperpage}{16}
\indexentry{gamma distribution (discrete)!number of categories|hyperpage}{16}
\indexentry{command-line options!\x{--nclasses}|hyperpage}{16}
\indexentry{gamma distribution (discrete)!shape parameter|hyperpage}{16}
\indexentry{command-line options!\x{--alpha}|hyperpage}{16}
\indexentry{gamma distribution (discrete)!mean vs. median|hyperpage}{16}
\indexentry{command-line options!\x{--use\_median}|hyperpage}{16}
\indexentry{command-line options!\x{--free\_rates}|hyperpage}{16}
\indexentry{command-line options!\x{--codpos}|hyperpage}{16}
\indexentry{NNI|hyperpage}{17}
\indexentry{SPR|hyperpage}{17}
\indexentry{command-line options!\x{--search}|hyperpage}{17}
\indexentry{input tree|hyperpage}{17}
\indexentry{user tree|hyperpage}{17}
\indexentry{command-line options!\x{--inputtree}|hyperpage}{17}
\indexentry{optimisation!topology|hyperpage}{17}
\indexentry{optimisation!substitution parameters|hyperpage}{17}
\indexentry{command-line options!\x{-o}|hyperpage}{17}
\indexentry{random tree|hyperpage}{17}
\indexentry{command-line options!\x{--rand\_start}|hyperpage}{17}
\indexentry{command-line options!\x{--n\_rand\_starts}|hyperpage}{17}
\indexentry{random number|hyperpage}{17}
\indexentry{command-line options!\x{--r\_seed}|hyperpage}{17}
\indexentry{likelihood!print site likelihood|hyperpage}{17}
\indexentry{command-line options!\x{--print\_site\_lk}|hyperpage}{17}
\indexentry{command-line options!\x{--print\_trace}|hyperpage}{18}
\indexentry{run ID|hyperpage}{18}
\indexentry{command-line options!\x{--run\_id}|hyperpage}{18}
\indexentry{command-line options!\x{--no\_memory\_check}|hyperpage}{18}
\indexentry{command-line options!\x{--no\_colalias}|hyperpage}{18}
\indexentry{command-line options!\x{--constrained\_lens}|hyperpage}{18}
\indexentry{command-line  options!\x{--constraint\_file}|hyperpage}{18}
\indexentry{command-line options!\x{--quiet}|hyperpage}{18}
\indexentry{command-line options!\x{--xml}|hyperpage}{19}
\indexentry{MPI|hyperpage}{19}
\indexentry{bootstrap!parallel|hyperpage}{19}
\indexentry{PHYLIP|hyperpage}{20}
\indexentry{NEXUS|hyperpage}{20}
\indexentry{sequential|hyperpage}{20}
\indexentry{interleaved|hyperpage}{20}
\indexentry{binary characters|hyperpage}{22}
\indexentry{Newick format|hyperpage}{24}
\indexentry{multiple data sets|hyperpage}{24}
\indexentry{PAML|hyperpage}{25}
\indexentry{XML|hyperpage}{28}
\indexentry{mixture models|hyperpage}{28}
\indexentry{partitionned analysis|hyperpage}{29}
\indexentry{data partitions|hyperpage}{29}
\indexentry{BEST|hyperpage}{30}
\indexentry{STEM|hyperpage}{30}
\indexentry{*BEAST|hyperpage}{30}
\indexentry{mixture   models|hyperpage}{35}
\indexentry{partitionned analysis|hyperpage}{35}
\indexentry{data partitions|hyperpage}{35}
\indexentry{XML options!{\tt phyml} component|hyperpage}{37}
\indexentry{XML options!{\tt topology} component|hyperpage}{38}
\indexentry{XML options!{\tt ratematrices} component|hyperpage}{39}
\indexentry{XML options!{\tt equfreqs} component|hyperpage}{40}
\indexentry{XML options!{\tt branchlengths} component|hyperpage}{40}
\indexentry{XML options!{\tt siterates} component|hyperpage}{41}
\indexentry{XML options!{\tt partitionelem}   component|hyperpage}{42}
\indexentry{XML options!{\tt mixtureelem} component|hyperpage}{42}
\indexentry{lg4x|hyperpage}{44}
\indexentry{PhyTime|hyperpage}{50}
\indexentry{serial sample|hyperpage}{52}
\indexentry{command-line options!\x{--calibration}|hyperpage}{52}
\indexentry{time scale|hyperpage}{53}
\indexentry{command-line options!\x{--chain\_len}|hyperpage}{53}
\indexentry{command-line options!\x{--sample\_freq}|hyperpage}{53}
\indexentry{command-line options!\x{--fastlk}|hyperpage}{53}
\indexentry{command-line options!\x{--no\_sequences}|hyperpage}{54}
\indexentry{command-line options!\x{--rate\_model}|hyperpage}{54}
\indexentry{Multidivtime|hyperpage}{54}
\indexentry{BEAST|hyperpage}{54}
\indexentry{Tracer|hyperpage}{54}
\indexentry{BEAST|hyperpage}{54}