\begin{thebibliography}{10}
\expandafter\ifx\csname url\endcsname\relax
  \def\url#1{\texttt{#1}}\fi
\expandafter\ifx\csname urlprefix\endcsname\relax\def\urlprefix{URL }\fi
\providecommand{\bibinfo}[2]{#2}
\providecommand{\eprint}[2][]{\url{#2}}

\bibitem{guindon03}
\bibinfo{author}{Guindon, S.} \& \bibinfo{author}{Gascuel, O.}
\newblock \bibinfo{title}{A simple, fast and accurate algorithm to estimate
  large phylogenies by maximum likelihood}.
\newblock \emph{\bibinfo{journal}{Systematic Biology}}
  \textbf{\bibinfo{volume}{52}}, \bibinfo{pages}{696--704}
  (\bibinfo{year}{2003}).

\bibitem{raxml}
\bibinfo{author}{Stamatakis, A.}
\newblock \bibinfo{title}{{RAxML-VI-HPC}: Maximum likelihood-based phylogenetic
  analyses with thousands of taxa and mixed models}.
\newblock \emph{\bibinfo{journal}{Bioinformatics}}
  \textbf{\bibinfo{volume}{22}}, \bibinfo{pages}{2688--2690}
  (\bibinfo{year}{2006}).

\bibitem{garli}
\bibinfo{author}{Zwickl, D.}
\newblock \emph{\bibinfo{title}{Genetic algorithm approaches for the
  phylogenetic analysis of large biological sequence datasets under the maximum
  likelihood criterion}}.
\newblock Ph.D. thesis, \bibinfo{school}{The University of Texas at Austin}
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\bibitem{jukes69}
\bibinfo{author}{Jukes, T.} \& \bibinfo{author}{Cantor, C.}
\newblock \bibinfo{title}{Evolution of protein molecules}.
\newblock In \bibinfo{editor}{Munro, H.} (ed.)
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\bibitem{kimura80}
\bibinfo{author}{Kimura, M.}
\newblock \bibinfo{title}{A simple method for estimating evolutionary rates of
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\newblock \emph{\bibinfo{journal}{Journal of Molecular Evolution}}
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\bibitem{felsenstein81a}
\bibinfo{author}{Felsenstein, J.}
\newblock \bibinfo{title}{Evolutionary trees from {DNA} sequences: a maximum
  likelihood approach}.
\newblock \emph{\bibinfo{journal}{Journal of Molecular Evolution}}
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\bibitem{phylip2}
\bibinfo{author}{Felsenstein, J.}
\newblock \emph{\bibinfo{title}{PHYLIP ({PHYL}ogeny {I}nference {P}ackage)
  version 3.6a2}} (\bibinfo{publisher}{Distributed by the author},
  \bibinfo{address}{Department of Genetics, University of Washington, Seattle},
  \bibinfo{year}{1993}).

\bibitem{hasegawa85}
\bibinfo{author}{Hasegawa, M.}, \bibinfo{author}{Kishino, H.} \&
  \bibinfo{author}{Yano, T.}
\newblock \bibinfo{title}{Dating of the {H}uman-{A}pe splitting by a molecular
  clock of mitochondrial-{DNA}}.
\newblock \emph{\bibinfo{journal}{Journal of Molecular Evolution}}
  \textbf{\bibinfo{volume}{22}}, \bibinfo{pages}{160--174}
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\bibitem{tamura93}
\bibinfo{author}{Tamura, K.} \& \bibinfo{author}{Nei, M.}
\newblock \bibinfo{title}{Estimation of the number of nucleotide substitutions
  in the control region of mitochondrial {DNA} in humans and chimpanzees}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{10}}, \bibinfo{pages}{512--526}
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\bibitem{lanave84}
\bibinfo{author}{Lanave, C.}, \bibinfo{author}{Preparata, G.},
  \bibinfo{author}{Saccone, C.} \& \bibinfo{author}{Serio, G.}
\newblock \bibinfo{title}{A new method for calculating evolutionary
  substitution rates}.
\newblock \emph{\bibinfo{journal}{Journal of Molecular Evolution}}
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  (\bibinfo{year}{1984}).

\bibitem{tavare86}
\bibinfo{author}{Tavar\'e, S.}
\newblock \bibinfo{title}{Some probabilistic and statistical problems on the
  analysis of {DNA} sequences}.
\newblock \emph{\bibinfo{journal}{Lectures on Mathematics in the Life
  Sciences}} \textbf{\bibinfo{volume}{17}}, \bibinfo{pages}{57--86}
  (\bibinfo{year}{1986}).

\bibitem{le08}
\bibinfo{author}{Le, S.} \& \bibinfo{author}{Gascuel, O.}
\newblock \bibinfo{title}{An improved general amino-acid replacement matrix}.
\newblock \emph{\bibinfo{journal}{Mol. Biol. Evol.}}
  \textbf{\bibinfo{volume}{25}}, \bibinfo{pages}{1307--1320}
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\bibitem{whelan01b}
\bibinfo{author}{Whelan, S.} \& \bibinfo{author}{Goldman, N.}
\newblock \bibinfo{title}{A general empirical model of protein evolution
  derived from multiple protein families using a maximum-likelihood approach}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{18}}, \bibinfo{pages}{691--699}
  (\bibinfo{year}{2001}).

\bibitem{dayhoff78}
\bibinfo{author}{Dayhoff, M.}, \bibinfo{author}{Schwartz, R.} \&
  \bibinfo{author}{Orcutt, B.}
\newblock \bibinfo{title}{A model of evolutionary change in proteins}.
\newblock In \bibinfo{editor}{Dayhoff, M.} (ed.)
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\bibitem{jones92}
\bibinfo{author}{Jones, D.}, \bibinfo{author}{Taylor, W.} \&
  \bibinfo{author}{Thornton, J.}
\newblock \bibinfo{title}{The rapid generation of mutation data matrices from
  protein sequences}.
\newblock \emph{\bibinfo{journal}{Computer Applications in the Biosciences
  (CABIOS)}} \textbf{\bibinfo{volume}{8}}, \bibinfo{pages}{275--282}
  (\bibinfo{year}{1992}).

\bibitem{henikoff92}
\bibinfo{author}{Henikoff, S.} \& \bibinfo{author}{Henikoff, J.}
\newblock \bibinfo{title}{Amino acid substitution matrices from protein
  blocks.}
\newblock \emph{\bibinfo{journal}{Proceedings of the National Academy of
  Sciences of the United States of America (PNAS)}}
  \textbf{\bibinfo{volume}{89}}, \bibinfo{pages}{10915--10919}
  (\bibinfo{year}{1992}).

\bibitem{adachi96}
\bibinfo{author}{Adachi, J.} \& \bibinfo{author}{Hasegawa, M.}
\newblock \bibinfo{title}{{MOLPHY} version 2.3. programs for molecular
  phylogenetics based on maximum likelihood}.
\newblock In \bibinfo{editor}{Ishiguro, M.} \emph{et~al.} (eds.)
  \emph{\bibinfo{booktitle}{Computer Science Monographs}}, \bibinfo{number}{28}
  (\bibinfo{publisher}{The Institute of Statistical Mathematics},
  \bibinfo{address}{Tokyo}, \bibinfo{year}{1996}).

\bibitem{dimmic02}
\bibinfo{author}{Dimmic, M.}, \bibinfo{author}{Rest, J.},
  \bibinfo{author}{Mindell, D.} \& \bibinfo{author}{Goldstein, D.}
\newblock \bibinfo{title}{{rtREV}: an amino acid substitution matrix for
  inference of retrovirus and reverse transcriptase phylogeny}.
\newblock \emph{\bibinfo{journal}{Journal of Molecular Evolution}}
  \textbf{\bibinfo{volume}{55}}, \bibinfo{pages}{65--73}
  (\bibinfo{year}{2002}).

\bibitem{adachi00}
\bibinfo{author}{Adachi, J.}, \bibinfo{author}{P., W.},
  \bibinfo{author}{Martin, W.} \& \bibinfo{author}{Hasegawa, M.}
\newblock \bibinfo{title}{Plastid genome phylogeny and a model of amino acid
  substitution for proteins encoded by chloroplast {DNA}}.
\newblock \emph{\bibinfo{journal}{Journal of Molecular Evolution}}
  \textbf{\bibinfo{volume}{50}}, \bibinfo{pages}{348--358}
  (\bibinfo{year}{2000}).

\bibitem{kosiol04}
\bibinfo{author}{Kosiol, C.} \& \bibinfo{author}{Goldman, N.}
\newblock \bibinfo{title}{Different versions of the {D}ayhoff rate matrix}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
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  (\bibinfo{year}{2004}).

\bibitem{muller00}
\bibinfo{author}{Muller, T.} \& \bibinfo{author}{Vingron, M.}
\newblock \bibinfo{title}{Modeling amino acid replacement.}
\newblock \emph{\bibinfo{journal}{Journal of Computational Biology}}
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  (\bibinfo{year}{2000}).

\bibitem{cao98}
\bibinfo{author}{Cao, Y.} \emph{et~al.}
\newblock \bibinfo{title}{Conflict among individual mitochondrial proteins in
  resolving the phylogeny of eutherian orders}.
\newblock \emph{\bibinfo{journal}{Journal of Molecular Evolution}}
  \textbf{\bibinfo{volume}{47}}, \bibinfo{pages}{307--322}
  (\bibinfo{year}{1998}).

\bibitem{gascuelNJ}
\bibinfo{author}{Gascuel, O.}
\newblock \bibinfo{title}{{BIONJ}: an improved version of the {NJ} algorithm
  based on a simple model of sequence data}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{14}}, \bibinfo{pages}{685--695}
  (\bibinfo{year}{1997}).

\bibitem{anisimova11}
\bibinfo{author}{Anisimova, M.}, \bibinfo{author}{Gil, M.},
  \bibinfo{author}{Dufayard, J.}, \bibinfo{author}{Dessimoz, C.} \&
  \bibinfo{author}{Gascuel, O.}
\newblock \bibinfo{title}{Survey of branch support methods demonstrates
  accuracy, power, and robustness of fast likelihood-based approximation
  schemes}.
\newblock \emph{\bibinfo{journal}{Systematic biology}}
  \textbf{\bibinfo{volume}{60}}, \bibinfo{pages}{685--699}
  (\bibinfo{year}{2011}).

\bibitem{anisimova06}
\bibinfo{author}{Anisimova, M.} \& \bibinfo{author}{Gascuel, O.}
\newblock \bibinfo{title}{Approximate likelihood-ratio test for branches: a
  fast, accurate, and powerful alternative}.
\newblock \emph{\bibinfo{journal}{Syst. Biol.}} \textbf{\bibinfo{volume}{55}},
  \bibinfo{pages}{539--552} (\bibinfo{year}{2006}).

\bibitem{posada01}
\bibinfo{author}{Posada, D.} \& \bibinfo{author}{Crandall, K.}
\newblock \bibinfo{title}{Selecting models of nucleotide substitution: an
  application to human immunodeficiency virus 1 (hiv-1)}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{18}}, \bibinfo{pages}{897--906}
  (\bibinfo{year}{2001}).

\bibitem{soubrier12}
\bibinfo{author}{Soubrier, J.} \emph{et~al.}
\newblock \bibinfo{title}{The influence of rate heterogeneity among sites on
  the time dependence of molecular rates}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  (\bibinfo{year}{2012}).

\bibitem{maddison97}
\bibinfo{author}{Maddison, D.}, \bibinfo{author}{Swofford, D.} \&
  \bibinfo{author}{Maddison, W.}
\newblock \bibinfo{title}{{NEXUS}: an extensible file format for systematic
  information}.
\newblock \emph{\bibinfo{journal}{Systematic Biology}}
  \textbf{\bibinfo{volume}{46}}, \bibinfo{pages}{590--621}
  (\bibinfo{year}{1997}).

\bibitem{yang94b}
\bibinfo{author}{Yang, Z.}
\newblock \bibinfo{title}{Maximum likelihood phylogenetic estimation from {DNA}
  sequences with variable rates over sites: approximate methods}.
\newblock \emph{\bibinfo{journal}{Journal of Molecular Evolution}}
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\bibitem{yang98}
\bibinfo{author}{Yang, Z.}
\newblock \bibinfo{title}{Likelihood ratio tests for detecting positive
  selection and application to primate lysozyme evolution}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{15}}, \bibinfo{pages}{568--573}
  (\bibinfo{year}{1998}).

\bibitem{yang00b}
\bibinfo{author}{Yang, Z.} \& \bibinfo{author}{Nielsen, R.}
\newblock \bibinfo{title}{Estimating synonymous and nonsynonymous substitution
  rates under realistic evolutionary models}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{17}}, \bibinfo{pages}{32--43}
  (\bibinfo{year}{2000}).

\bibitem{yang02}
\bibinfo{author}{Yang, Z.} \& \bibinfo{author}{Nielsen, R.}
\newblock \bibinfo{title}{Codon-substitution models for detecting molecular
  adaptation at individual sites along specific lineages}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{19}}, \bibinfo{pages}{908--917}
  (\bibinfo{year}{2002}).

\bibitem{guindon04}
\bibinfo{author}{Guindon, S.}, \bibinfo{author}{Rodrigo, A.},
  \bibinfo{author}{Dyer, K.} \& \bibinfo{author}{Huelsenbeck, J.}
\newblock \bibinfo{title}{Modeling the site-specific variation of selection
  patterns along lineages}.
\newblock \emph{\bibinfo{journal}{Proceedings of the National Academy of
  Sciences of the United States of America (PNAS)}}
  \textbf{\bibinfo{volume}{101}}, \bibinfo{pages}{12957--12962}
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\bibitem{degnan09}
\bibinfo{author}{Degnan, J.} \& \bibinfo{author}{Rosenberg, N.}
\newblock \bibinfo{title}{Gene tree discordance, phylogenetic inference and the
  multispecies coalescent}.
\newblock \emph{\bibinfo{journal}{Trends in Ecology \& Evolution}}
  \textbf{\bibinfo{volume}{24}}, \bibinfo{pages}{332--340}
  (\bibinfo{year}{2009}).

\bibitem{best}
\bibinfo{author}{Liu, L.}
\newblock \bibinfo{title}{Best: Bayesian estimation of species trees under the
  coalescent model}.
\newblock \emph{\bibinfo{journal}{Bioinformatics}}
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  (\bibinfo{year}{2008}).

\bibitem{stem}
\bibinfo{author}{Kubatko, L.}, \bibinfo{author}{Carstens, B.} \&
  \bibinfo{author}{Knowles, L.}
\newblock \bibinfo{title}{Stem: species tree estimation using maximum
  likelihood for gene trees under coalescence}.
\newblock \emph{\bibinfo{journal}{Bioinformatics}}
  \textbf{\bibinfo{volume}{25}}, \bibinfo{pages}{971--973}
  (\bibinfo{year}{2009}).

\bibitem{startbeast}
\bibinfo{author}{Heled, J.} \& \bibinfo{author}{Drummond, A.}
\newblock \bibinfo{title}{Bayesian inference of species trees from multilocus
  data}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{27}}, \bibinfo{pages}{570--580}
  (\bibinfo{year}{2010}).

\bibitem{matsen07}
\bibinfo{author}{Matsen, F.} \& \bibinfo{author}{Steel, M.}
\newblock \bibinfo{title}{Phylogenetic mixtures on a single tree can mimic a
  tree of another topology}.
\newblock \emph{\bibinfo{journal}{Systematic biology}}
  \textbf{\bibinfo{volume}{56}}, \bibinfo{pages}{767--775}
  (\bibinfo{year}{2007}).

\bibitem{shimodaira99}
\bibinfo{author}{Shimodaira, H.} \& \bibinfo{author}{Hasegawa, M.}
\newblock \bibinfo{title}{Multiple comparisons of log-likelihoods with
  applications to phylogenetic inference}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{16}}, \bibinfo{pages}{1114--1116}
  (\bibinfo{year}{1999}).

\bibitem{lg4x}
\bibinfo{author}{Le, S.~Q.}, \bibinfo{author}{Dang, C.~C.} \&
  \bibinfo{author}{Gascuel, O.}
\newblock \bibinfo{title}{Modeling protein evolution with several amino acid
  replacement matrices depending on site rates}.
\newblock \emph{\bibinfo{journal}{Molecular Biology and Evolution}}
  \textbf{\bibinfo{volume}{29}}, \bibinfo{pages}{2921--2936}
  (\bibinfo{year}{2012}).

\bibitem{kishino01}
\bibinfo{author}{Kishino, H.}, \bibinfo{author}{Thorne, J.} \&
  \bibinfo{author}{Bruno, W.}
\newblock \bibinfo{title}{{{P}erformance of a divergence time estimation method
  under a probabilistic model of rate evolution}}.
\newblock \emph{\bibinfo{journal}{Mol. Biol. Evol.}}
  \textbf{\bibinfo{volume}{18}}, \bibinfo{pages}{352--361}
  (\bibinfo{year}{2001}).

\bibitem{guindon12}
\bibinfo{author}{Guindon, S.}
\newblock \bibinfo{title}{From trajectories to averages: an improved
  description of the heterogeneity of substitution rates along lineages.}
\newblock \emph{\bibinfo{journal}{Systematic Biology}}  (\bibinfo{year}{2012}).

\bibitem{posada98}
\bibinfo{author}{Posada, D.} \& \bibinfo{author}{Crandall, K.}
\newblock \bibinfo{title}{Modeltest: testing the model of {DNA} substitution}.
\newblock \emph{\bibinfo{journal}{Bioinformatics}}
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  (\bibinfo{year}{1998}).

\bibitem{abascal05}
\bibinfo{author}{Abascal, F.}, \bibinfo{author}{Zardoya, R.} \&
  \bibinfo{author}{Posada, D.}
\newblock \bibinfo{title}{Prottest: selection of best-fit models of protein
  evolution}.
\newblock \emph{\bibinfo{journal}{Bioinformatics}}
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  (\bibinfo{year}{2005}).

\bibitem{galtier04}
\bibinfo{author}{Galtier, N.} \& \bibinfo{author}{Jean-Marie, A.}
\newblock \bibinfo{title}{Markov-modulated {M}arkov chains and the covarion
  process of molecular evolution}.
\newblock \emph{\bibinfo{journal}{Journal of Computational Biology}}
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  (\bibinfo{year}{2004}).

\end{thebibliography}