aculasso
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monkey business
Posts: 13
Buenos Aires - Argentina
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There is the console output:
---- RUNNING MOLECULAR CLOCK ANALYSIS WITH DATED TIPS---- The underlying methodology developed by Andrew Rambaut is discussed in Bioinformatics 16(4): 395-399 The following data was read: 6 species:{NOV1998_16301,JUL1999_16524,MAR2000_16772,OCT2001_17356,FEB2002_17490,A GO2006_19107}; Total Sites:594; Distinct Sites:39 What units are the dates measured in (e.g. months)? This is only used for reporting the results.days Read the following dates: Nov1998_16301: 16301 days Jul1999_16524: 16524 days Mar2000_16772: 16772 days Oct2001_17356: 17356 days Ago2006_19107: 19107 days Feb2002_17490: 17490 days
CPU time taken: 0.406 seconds.
*-----------------------------------------------------------* RESULTS WITHOUT THE CLOCK: Log Likelihood = -1144.61222607557; Shared Parameters: CG=0.421889 CT=0.816344 GT=0.160682 AT=0.614661 AC=0.615745
Tree givenTree=(Nov1998_16301:0.00675717,Jul1999_16524:0,(Mar2000_16772:0.0106789,((O ct2001_17356:0.00512315,Ago2006_19107:0.0309416)Node6:0.00497006,Feb2002_17490:0 .00604879)Node5:0.00777962)Node3:0.0201417); *-----------------------------------------------------------*
RESULTS WITH DATED TIPS CLOCK: Log-likelihood: -1152.64186266955 CPU time taken: 0.922 seconds.
*-----------------------------------------------------------*
-2(Ln Likelihood Ratio)=16.0593 Constrained parameters:4 Asymptotic p-value:0.00294065 Tree with branch lengths scaled in days: (Nov1998_16301:332.836,Jul1999_16524:555.836,(Mar2000_16772:270.076,((Oct2001_17 356:208.657,Ago2006_19107:1959.66):192.178,Feb2002_17490:534.835):453.241):533.7 61)
Root of the tree placed at 15968.2(95% CI: 15797.7,16089.9) days
Substitution rate estimated at 1.83759e-05(95% CI: 0.138983,0.237546) subs per days per site
====================== Also, I´ve attached 2 comma separated value files with LF (constrained and unconstrainde) (Zipped).
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