Sergey Svishchev
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6485d5b37a
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Follow redirects.
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2007-07-15 18:33:16 +00:00 |
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Roland Illig
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1ee539a984
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Added RMD160 checksums.
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2005-09-28 06:41:05 +00:00 |
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David
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9a0b6ff141
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changed (dollar)f to (dollar){f}
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2005-04-19 23:45:57 +00:00 |
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Todd Vierling
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5f60a41bb5
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Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.
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2005-04-11 21:09:34 +00:00 |
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David
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1db0597bf1
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initial import of patch-ac, which adds a main to make libg2c happy
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2005-03-31 20:47:51 +00:00 |
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David
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b7c9f9fecf
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updated to reflect new patch aa and ab
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2005-03-18 20:02:03 +00:00 |
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David
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f2ea154084
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patch now patches treeutils.h, instead of main.c
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2005-03-18 19:58:00 +00:00 |
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David
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56d406bd5c
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added CXX = g++ to treeutils.h
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2005-03-18 19:55:31 +00:00 |
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David
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213af65342
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This is a program for estimating rates (r8s) of molecular evolution and divergence times on a phylogenetic tree. It implements several methods for estimating these parameters ranging from fairly standard maximum likelihood methods in the context of global or local molecular clocks to more experimental semiparametric and nonparametric methods that relax the stringency of the clock assumption using smoothing methods. Its starting point is a given phylogenetic tree and a given set of estimated branch lengths (numbers of substitutions along each branch). In addition one or more calibration points can be added to permit scaling of rates and times to real units. These calibrations can take one of two forms: assignment of a fixed age to a node, or enforcement of a minimum or maximum age constraint on a node, which is generally a better reflection of the information content of fossil evidence. Terminal nodes are permitted to occur at any point in time, allowing investigation of rate variation in phylogenies such as those obtained from serial samples of viral lineages through time. Finally, it is possible to assign all divergence times (perhaps based on outside estimates of divergence times) and examine molecular rate variation under several models of smoothing.
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2005-01-16 18:54:25 +00:00 |
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