20 lines
1.3 KiB
Plaintext
20 lines
1.3 KiB
Plaintext
This is a program for estimating rates ("r8s") of molecular evolution
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and divergence times on a phylogenetic tree. It implements several
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methods for estimating these parameters ranging from fairly standard
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maximum likelihood methods in the context of global or local molecular
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clocks to more experimental semiparametric and nonparametric methods
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that relax the stringency of the clock assumption using smoothing
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methods. Its starting point is a given phylogenetic tree and a given
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set of estimated branch lengths (numbers of substitutions along each
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branch). In addition one or more calibration points can be added to
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permit scaling of rates and times to real units. These calibrations
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can take one of two forms: assignment of a fixed age to a node, or
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enforcement of a minimum or maximum age constraint on a node, which is
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generally a better reflection of the information content of fossil
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evidence. Terminal nodes are permitted to occur at any point in time,
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allowing investigation of rate variation in phylogenies such as those
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obtained from "serial" samples of viral lineages through time.
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Finally, it is possible to assign all divergence times (perhaps based
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on outside estimates of divergence times) and examine molecular rate
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variation under several models of smoothing.
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