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Ziheng Yang, 27 January 2003
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This folder contains files for the local-clock likelihood analysis of Yoder
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The clock models are re-written. Note that the fossil calibration
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points are specified using the symbol '@' in the tree file; the symbol
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is used in the same way as the more familiar symbol ':' for branch
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lengths. TipDate models are implemented using @ in the sequence name
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to specify the date of determination of the sequence. Look at the
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examples/TipDate folder for an example. Local clock models are
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specified by assigning rates to branches, using the symbol # to label
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the branch/node. The symbol $ is used as a clade label; $ stands
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for the capital greek symbol \Delta, which looks somewhat like a clade.
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Use clock = 2 for local clock models. For models of multiple genes,
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clock = 3 represents the "combined analysis" in Yang & Yoder (2003).
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The program assumes the same set of species and the same phylogeny at
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clock = 1: global clock, deals with TipDate with no or many fossils,
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ignores branch rates (#) in tree if any.
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= 2: local clock models, as (1) above, but requires branch
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= 3: as (2) above, but requires Mgene and option G in sequence
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The following describes specifications in baseml.ctl to duplicate the
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ML results in tables 4 and 5 of Yang and Yoder (2003). Note that the
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ML analysis uses the ingroup sequences only, and the assumed ingroup
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tree is rooted. In the Bayes analysis of that paper, Thorne's program
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(estbranches) requires an outgroup to root the ingroup tree. The
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"JeffNode" node numbering corresponds to the the node numbering by
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Jeff Thorne's Bayes MCMC programs divtime5b and multidivtime, used in
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our paper. My output is correct only if you do what we did, that is,
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only if you use the outgroup in Jeff's estbranches program and do not
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use the outgroup sequences in the baseml ML analysis. Note that the
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node numbering in Tables 4 and 5 of that paper is according to Jeff's
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programs divtime5b and multidivtime.
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JC69 analysis in Tables 4 and 5
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===============================
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Columns b, c, d. Use optoin GC on the first line of the sequence data file
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The tree in the tree file has seven @ specifying seven calibration
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dates. Use Mgene = 1 for separate analysis. Other options are
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These options should generate the three columns in one analysis. The
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option clock = 1 has precedence over the branch rate labels # in the
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tree file. So clock = 1 above means that the model is a global clock
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and the rate labels # are ignored.
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Columns b, c, d in table 5 (local clock analysis). If you choose
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clock = 2 in the above, you should recover results for the local clock
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Column i in table 4 (combined global clock analysis under JC69) is
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produced by the following options:
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Column i in table 5 (combined local clock analysis under JC69) is
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produced by changing clock = 3 in the above.
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F84G analysis in Tables 4 and 5
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===============================
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Use the following to specify the gamma model.
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alpha = 0.5 (or any other initial value)
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Columns f, g, h in table 4 (global clock analysis). Use optoin GC on
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the first line of the sequence data file. The tree in the tree file
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has seven @ specifying seven calibration dates. Use Mgene = 1 for
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separate analysis. Other options are
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alpha = 0.5 (or any other initial value)
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Columns f, g, h in table 5 (F84G local clock analysis). Change clock
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Column j in table 4 (combined global clock analysis under F84G) is
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produced by the following options:
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Column j in table 5 (combined local clock analysis under F84G) is
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produced by setting clock = 3 in the above.
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examples/MouseLemurs/README.txt
