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• Character type 1: ANY DNA strict DNA broad RNA strict RNA broad AA strict AA broad Binary Multistate unordered Multistate ordered Continuous unbounded Continuous nonnegative Continuous positive Continuous bounded Frequency/proportion Continuous 1D range Continuous 1D distribution Continuous multidimensional range None ?
• Criterion: ANY Parsimony Likelihood Bayesian Least squares ?
• Tree type: ANY Rooted, binary, complete tree Rooted, binary, incomplete tree Unrooted, binary, complete tree Unrooted, binary, incomplete tree Rooted, polytomies, complete tree Rooted, polytomies, incomplete tree Unrooted, polytomies, complete tree Unrooted, polytomies, incomplete tree Galled tree General network, unknown branch widths General network, known branch widths ?
• Elements above this line appear on tree (first is closest to root, and so on)
• General question: ANY Reconstruct ancestor(s) Correlate character states Correlate character rates Correlate character state(s) with character rate(s) Simulate states Tree-only diversification/coalescence methods Tree+Data diversification/coalescence methods Tree-tree correlation Display tree Make tree proportional to time Parameter estimation or model selection for character model Adjust for tree uncertainty ?
• Specific question: ANY Reconstruct state at one node Reconstruct state at all internal nodes Reconstruct state everywhere on tree Correlate states of two characters, same character type Correlate states of two characters, different character types Correlate states of one character of one type with states of multiple characters of the same type Correlate states of one character of one type with states of multiple characters of a different type Correlate states of multiple characters of one type with states of multiple characters of the same type Correlate states of multiple characters of one type with states of multiple characters of a different type Correlate rates of two characters, same character type Correlate rates of two characters, different character types Correlate rates of one character of one type with rates of multiple characters of the same type Correlate rates of one character of one type with rates of multiple characters of a different type Correlate rates of multiple characters of one type with rates of multiple characters of the same type Correlate rates of multiple characters of one type with rates of multiple characters of a different type Correlate state of one character with rate of another character, same character type Correlate state of one character with rate of another character, different character types Correlate state of one character of one type with rates of multiple characters of the same type Correlate state of one character of one type with rates of multiple characters of a different type Correlate states of multiple characters of one type with rates of multiple characters of the same type Correlate states of multiple characters of one type with rates of multiple characters of a different type Compare model fits for single character Compare model fits for multiple characters of the same type Compare model fits for a pair of characters of the same type Compare model fits for a pair of characters of different types Estimate parameters using a single character Estimate parameters using multiple characters of the same type Estimate parameters using a pair of characters of the same type Estimate parameters using a pair of characters of different types Estimate local speciation and extinction rates Estimate global diversification rate Estimate global speciation and extinction rates Estimate local diversification rates Estimate species limits Influence of one trait on diversification rate Do these two groups have significantly different rates of diversification Compare fits/scores of diversification models Make branches proportional to time using just information from topology (no starting branch lengths or fossils) Make branches proportional to time using just initial branch lengths Make branches proportional to time using just calibration information Make branches proportional to time using initial branch lengths and calibration information Simulate states for independently-evolving characters at tips only Simulate states for independently-evolving characters at tips and nodes only Simulate states for independently-evolving characters everywhere along a tree Simulate states for coevolving characters at tips Simulate states for coevolving characters at tips and nodes only Simulate states for coevolving characters everywhere along tree Resolve multifurcating (non-binary) tree, topology only Resolve multifurcating (non-binary) tree, topology and branch lengths only Integrate over a set of trees Add missing species Create branch lengths Show topology only Show tree with branch lengths Show tree with numerical branch label Show tree with multiple numerical branch labels Show tree with branch colors, one color per branch Show tree with branch colors, multiple colors per branch Show tree with charts on nodes Show tree with charts on branches ?
• Branch length type: ANY Unknown Equal Grafen Time-proportional Time-calibrated Discrete-char parsimony Discrete-char likelihood Discrete-char Bayesian Discrete-char distance Continuous-char parsimony Continuous-char likelihood Continuous-char Bayesian Continuous-char distance ?
• Method: ANY Fitch ancestral state reconstruction (Wagner/unordered parsimony) Independent contrasts Farris ancestral state reconstruction (ordered parsimony) Discrete trait ancestral state optimum Concentrated changes test Correlated change in two variables (Pagel Discrete) Multiple rate Brownian motion, censored approach Multiple rate Brownian motion, noncensored approach Discrete trait ancestral state marginal probabilities Ornstein-Uhlenbeck Hansen version Ornstein-Uhlenbeck Butler-King version Paired sister group sign test Sister group diversification test Hey diversification G and C models Birth-death parameter estimation all species Birth-death parameter estimation random subsample of species Stochastic Yule with cladograms Deterministic branching rate estimation BiSSE Diversification with stochastic character mapping Multiple Yule model fitting OU transform (Blomberg et a.) ACDC transform (Blomberg et al.) Permutation for phylogenetic signal Estimation of phylogenetic signal (Blomberg et al. K) Kappa transform (Pagel) Lambda transform (Pagel) Delta transform (Pagel) Single rate Brownian motion or Ornstein-Uhlenbeck Generate random trees Generalized Linear Model (GLM) Rectangular tree, topology only Rectangular tree, branch length Rectangular tree, single label on branch Rectangular tree, multiple labels on branch Rectangular tree, one color per branch Rectangular tree, multiple colors per branch Rectangular tree, chart on node Rectangular tree, chart on branches Straight line tree, topology only Straight line tree, branch lengths Straight line tree, single label on branch Straight line tree, multiple labels on branch Straight line tree, chart on node Straight line tree, chart on branches Circular tree, topology only Circular tree, branch lengths Circular tree, single label on branch Circular tree, multiple labels on branch Circular tree, chart on node Circular tree, chart on branches Generalized estimating equations (GEE) Disparity through time plot Morphological disparity index Gamma statistic (Pybus & Harvey) Comparison of 5 macroevolutionary models Comparison of 9 macroevolutionary models Stochastic character mapping Rate shift Auteur alpha NRS test Medusa Multivariate multirate Brownian motion Disparity through time plot ?
• Program: ANY Brownie Mesquite PDAP PHYLIP OUCH geiger COMET ape SIMMAP AUTEUR ?
• Application type: ANY standalone application command line standalone application with GUI web application R package Matlab/Octave script Mesquite module ?
• Branch length type: ANY Unknown Equal Grafen Time-proportional Time-calibrated Discrete-char parsimony Discrete-char likelihood Discrete-char Bayesian Discrete-char distance Continuous-char parsimony Continuous-char likelihood Continuous-char Bayesian Continuous-char distance ?
• Character type 2: ANY DNA strict DNA broad RNA strict RNA broad AA strict AA broad Binary Multistate unordered Multistate ordered Continuous unbounded Continuous nonnegative Continuous positive Continuous bounded Frequency/proportion Continuous 1D range Continuous 1D distribution Continuous multidimensional range None
• Character type 3: ANY DNA strict DNA broad RNA strict RNA broad AA strict AA broad Binary Multistate unordered Multistate ordered Continuous unbounded Continuous nonnegative Continuous positive Continuous bounded Frequency/proportion Continuous 1D range Continuous 1D distribution Continuous multidimensional range None
• Data format: ANY NEXUS PHYLIP FASTA GenBank OUCH ?
• Platform: ANY Mac OS 10.5 Mac OS 10.4 Mac OS 10.3 Mac OS 9 (Classic) Windows Vista Windows XP Windows 2000 Windows 98 Windows NT 4 Windows 95 MS-DOS Cygwin under Windows Linux Unix Mac OS 10.2 Mac OS 10.1 ?
• Tree format: ANY newick OUCH NEXUS PHYLIP SIMMAP phylo4 phylo ?