Physher is a maximum likelihood-based method for estimating evolutionary rates and divergence times from genetic, amino acid, codon, and generic data. Phylogenetic trees should be open with Figtree from this website or Seqotron.
For more details about the configuration file and command line arguments see the wiki
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Substitution models:
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Nucleotide: Reversible: GTR, HKY, K80, and JC69 + any models using encoding 00000 ... 01234. Non reversible: UREV (stationary) and NONSTAT (non stationary).
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Codon: GY94.
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Amino acid: Dayhoff, LG, and WAG.
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General: custom state space (e.g. phylogeography).
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Rate heterogeneity among sites:
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Gamma distributed.
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Proportion of invariant site.
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Molecular clock:
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No clock
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Strict clock: constant rate across lineages.
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Local clock: monophyletic lineages evolve at the same rate.
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Discrete clock: a discrete distribution of rates is assigned to lineages without any restriction on the rate distribution.
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Search algorithms for clock models:
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Greedy algorithm (local clock only).
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Genetic algorithm (discrete clock only).
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Topology search:
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Nearest neighbor interchange (NNI)
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Confidence intervals
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Non-parametric bootstrap (Normal and percentile) using bootstrap program (only available for strict clock models).
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Model averaging of divergence times and substitution rate
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Using modelavg program (only available using the genetic algorithm with discrete clocks).
- bootstrap: calculate confidence intervals using bootstrap trees generated by a strict clock with physher. Every tree need to have the same topology.
- simultron: simulate nucleotide data given a fixed tree topology.
- modelavg: model average of trees generated by genetic algorithm with a discrete clock.
Fourment M and Holmes EC. Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data. BMC Evolutionary Biology 14:163, 2014.