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30 October 2000, 24 January 2003 (modified), Ziheng Yang
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Rambaut's TipDate model is implemented using the symbol @ in the
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sequence data file to specify the date of determination of each
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sequence. Note that the symbol and the date are considered part of
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the sequence name, so that they should be used in the tree file. Note
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that to use the TipDate models, every sequence in the data file must
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have a known date, and the program does not work if some sequences are
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dated while other are not. Have a look at both TipDate.phy and
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TipDate.trees for the notation. The sequence data file TipDate.phy is
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directly usable by Rambaut's TipDate program, so you can use the @
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notation to prepare a file readable by both programs. Then choose
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clock = 1 (global clock) to run the TipDate model. To allow local
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branch rates, you can use the symbol # in the tree file. Look at the
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files in the examples/mouselemurs/ for implementation of local clock
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The rest of the file contains two parts, as follows.
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(A) Results from running Andrew Rambaut's TipDate program.
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(B) baseml HKY85 global clock (clock=1)
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Rambaut, A. 2000. Estimating the rate of molecular evolution: incorporating
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non-comptemporaneous sequences into maximum likelihood phylogenetics.
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Bioinformatics 16:395-399.
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Yang, Z., and A. D. Yoder. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Syst. Biol. 52:705-716.
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*************************************************
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(A) Results from Andrew Rambaut's TipDate program
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Note that I changed the file name from Andrew's example.phy to
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TipDate.phy. The command to run Andrew's TipDate is
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tipdate -mHKY +s -v < TipDate.phy >out
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Analysis of trees with dated tips - TipDate
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(c) Copyright, 1997-2001 Andrew Rambaut
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Department of Zoology, University of Oxford
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South Parks Road, Oxford OX1 3PS, U.K.
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Calculating likelihood of user supplied tree,
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iterating to find maximum likelihood branch lengths,
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assuming a molecular clock with dated taxa (SRDT model).
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Taxa dates range between 56 and 94,
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estimating the absolute rate of molecular evolution.
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and using the rate of change rate supplied = 0.000000
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Rate homogeneity assumed.
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estimating ML transition/transversion ratio
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estimating base frequences from data
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frequencies = A:0.307506 C:0.187681 G:0.272450 T:0.232363
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Tree in units of time:
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(((((((((Brazi@82:1.52387882,(ElSal@83:0.86955431,NewCal@84:1.86955431):1.65432451):0.00001293,Mexico@84:3.52389175):1.37695033,ElSal@94:14.90084208):1.90479505,(PRico@86:7.72505490,Tahiti@85:6.72505490):1.08058224):0.00000000,Tahiti@79:1.80563713):4.79198989,Indon@77:4.59762703):1.05572925,Indon@76:4.65335628):39.69611913,(((Philip@64:3.86265651,Philip@84:23.86265651):7.33594953,Philip@56:3.19860604):13.22151465,(SLanka@78:21.63676446,(Thai@78:6.99850875,Thai@84:12.99850875):14.63825571):16.78335624):7.92935471):7.55525759,Thai@63:38.90473300);
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Estimated value of Ts/Tv: 8.901642 (kappa=17.022524)
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Estimated absolute rate of molecular evolution: 0.00077366
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Absolute age of tree: 69.904733 (in the same units as the taxon dates,
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measured to the most recent tip).
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Tree ln Likelihood = -3849.932714
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Time taken - core: 4.827, total: 4.887 seconds
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BASEML (in paml 3.13b, February 2003) TipDate.phy HKY85 Global clock
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TREE # 1: (((((((((1, (2, 7)), 6), 3), (11, 14)), 13), 5), 4), (((8, 10), 9), (12, (16, 17)))), 15); MP score: 312.00
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lnL(ntime: 17 np: 18): -3849.932737 +0.000000
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18..19 19..20 20..21 21..22 22..23 23..24 24..25 25..26 26..1 26..27 27..2 27..7 25..6 24..3 23..28 28..11 28..14 22..13 21..5 20..4 19..29 29..30 30..31 31..8 31..10 30..9 29..32 32..12 32..33 33..16 33..17 18..15
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0.36792 0.32816 0.11923 0.11367 0.08845 0.08845 0.07843 0.07118 0.07118 0.06247 0.08276 0.28642 0.21684 0.17823 0.19809 0.12105 0.14699 17.02252
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0.03565 0.03264 0.00829 0.00795 0.00479 0.00480 0.00702 0.00454 0.00454 0.00463 0.00550 0.02551 0.00860 0.01028 0.02008 0.01185 0.01934 2.97312
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Note: mutation rate is not applied to tree length. Tree has times, for TreeView
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(((((((((Brazi@82, (ElSal@83, NewCal@84)), Mexico@84), ElSal@94), (PRico@86, Tahiti@85)), Tahiti@79), Indon@77), Indon@76), (((Philip@64, Philip@84), Philip@56), (SLanka@78, (Thai@78, Thai@84)))), Thai@63);
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(((((((((Brazi@82: 1.523930, (ElSal@83: 0.869570, NewCal@84: 1.869570): 1.654360): 0.000002, Mexico@84: 3.523932): 1.376981, ElSal@94: 14.900913): 1.904789, (PRico@86: 7.725130, Tahiti@85: 6.725130): 1.080572): 0.000005, Tahiti@79: 1.805707): 4.792057, Indon@77: 4.597763): 1.055732, Indon@76: 4.653495): 39.696751, (((Philip@64: 3.862769, Philip@84: 23.862769): 7.335980, Philip@56: 3.198749): 13.222004, (SLanka@78: 21.637157, (Thai@78: 6.998700, Thai@84: 12.998700): 14.638457): 16.783596): 7.929492): 7.555240, Thai@63: 38.905485);
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Detailed output identifying parameters
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Substitution rate is per time unit
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(JeffNode is for Thorne's multidivtime. ML analysis uses ingroup data only.)
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Node 1 (Jeffnode 0) Time 82.00
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Node 2 (Jeffnode 1) Time 83.00
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Node 3 (Jeffnode 2) Time 94.00
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Node 4 (Jeffnode 3) Time 76.00
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Node 5 (Jeffnode 4) Time 77.00
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Node 6 (Jeffnode 5) Time 84.00
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Node 7 (Jeffnode 6) Time 84.00
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Node 8 (Jeffnode 7) Time 64.00
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Node 9 (Jeffnode 8) Time 56.00
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Node 10 (Jeffnode 9) Time 84.00
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Node 11 (Jeffnode 10) Time 86.00
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Node 12 (Jeffnode 11) Time 78.00
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Node 13 (Jeffnode 12) Time 79.00
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Node 14 (Jeffnode 13) Time 85.00
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Node 15 (Jeffnode 14) Time 63.00
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Node 16 (Jeffnode 15) Time 78.00
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Node 17 (Jeffnode 16) Time 84.00
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Node 18 (Jeffnode 32) Time 24.09 +- 6.73
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Node 19 (Jeffnode 31) Time 31.65 +- 6.17
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Node 20 (Jeffnode 30) Time 71.35 +- 1.57
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Node 21 (Jeffnode 29) Time 72.40 +- 1.51
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Node 22 (Jeffnode 28) Time 77.19 +- 0.91
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Node 23 (Jeffnode 27) Time 77.19 +- 0.91
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Node 24 (Jeffnode 26) Time 79.10 +- 1.33
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Node 25 (Jeffnode 25) Time 80.48 +- 0.86
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Node 26 (Jeffnode 24) Time 80.48 +- 0.86
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Node 27 (Jeffnode 23) Time 82.13 +- 0.88
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Node 28 (Jeffnode 22) Time 78.27 +- 1.04
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Node 29 (Jeffnode 21) Time 39.58 +- 4.82
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Node 30 (Jeffnode 20) Time 52.80 +- 1.63
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Node 31 (Jeffnode 19) Time 60.14 +- 1.95
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Node 32 (Jeffnode 18) Time 56.36 +- 3.80
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Node 33 (Jeffnode 17) Time 71.00 +- 2.25
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Parameters (kappa) in the rate matrix (HKY85) (Yang 1994 J Mol Evol 39:105-111):
added
removed
examples/TipDate/README.txt
