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bugzilla and datedtipmolecularclock.bf (Read 1619 times)
gnolasco
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bugzilla and datedtipmolecularclock.bf
Feb 7th, 2007 at 2:01am
 
Hi Sergei,
I tried to register in bugzilla but never received the password, so here goes the bug(?)

When using datedtipmolecularclock, if i repeat twice and sucessively the same analysis I get different results. Even if I kill all the information that may reside in the console and object inspector. If I close the programme and reopen and reload the data I get the same values as the first time. An example of the resulst is below.
Thanks for any clues.
Gustavo
gnolasco@ualg.pt

************************************

HYPHY 0.9920070130beta(MP) for Windows (Win32) console saved on Tue Feb  6 17:39:26 2007


Loaded 23 model templates from C:\Programas\HYPHY_Win32\SubstitutionModels
Loaded 12 genetic code tables from C:\Programas\HYPHY_Win32\GeneticCodes
One  Intel x86 architecture  processor detected

Please cite S.L. Kosakovsky Pond, S. D. W. Frost and S.V. Muse. (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21: 676-679 if you use HyPhy in a publication
If you are a new HyPhy user, the tutorial located at http://www.hyphy.org/docs/HyphyDocs.pdf may be a good starting point.

---- 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:
10 species:{199_23_2006,199_26_2006,212_15_2006,196_13_2006,212_8_2006,196_1_2004,2
11_32_2004,211_13_2006,212_16_2006,15_118_1995};
Total Sites:630;
Distinct Sites:15
What units are the dates measured in (e.g. months)? This is only used for reporting the results.y
Read the following dates:
199_23_2006:      2006      y
199_26_2006:      2006      y
212_15_2006:      2006      y
211_13_2006:      2006      y
15_118_1995:      1995      y
211_32_2004:      2004      y
196_13_2006:      2006      y
212_8_2006:      2006      y
212_16_2006:      2006      y
196_1_2004:      2004      y

CPU time taken: 0.047 seconds.

*-----------------------------------------------------------*
RESULTS WITHOUT THE CLOCK:
Log Likelihood = -972.184380018069;
Shared Parameters:
R=0.198097

Tree givenTree=(((((199_23_2006:0.00158835,199_26_2006:0.00318115)Node4:0,212_15_2006
:0.00158823)Node3:0,(211_13_2006:0.00158804,15_118_1995:3.45099e-31)Node8:3.4509
9e-31)Node2:3.45099e-31,(211_32_2004:3.45099e-31,(196_13_2006:0.00318414,212_8_2
006:0.00318453)Node13:0)Node11:0)Node1:3.45099e-31,212_16_2006:0.0031839,196_1_2
004:0.00476653);
*-----------------------------------------------------------*

RESULTS WITH DATED TIPS CLOCK:
Log-likelihood: -976.163122950982
CPU time taken: 0.188 seconds.

*-----------------------------------------------------------*

-2(Ln Likelihood Ratio)=7.95749
Constrained parameters:8
Asymptotic p-value:0.437634
Tree with branch lengths scaled in y:
(((((199_23_2006:1523.12,199_26_2006:1523.12):0,212_15_2006:1523.12):0,(211_13_2
006:1141.35,15_118_1995:1130.35):381.766):0,(211_32_2004:1521.12,(196_13_2006:15
23.12,212_8_2006:1523.12):0):0):379.086,212_16_2006:1902.2,196_1_2004:1900.2)

Root of the tree placed at 103.796(95% CI: -883.329,786.737) y

Substitution rate estimated at 1.3911e-06(95% CI: 0.000785508,0.00225791) subs per y per site


---- 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:
10 species:{199_23_2006,199_26_2006,212_15_2006,196_13_2006,212_8_2006,196_1_2004,2
11_32_2004,211_13_2006,212_16_2006,15_118_1995};
Total Sites:630;
Distinct Sites:15
What units are the dates measured in (e.g. months)? This is only used for reporting the results.y
Read the following dates:
199_23_2006:      2006      y
199_26_2006:      2006      y
212_15_2006:      2006      y
211_13_2006:      2006      y
15_118_1995:      1995      y
211_32_2004:      2004      y
196_13_2006:      2006      y
212_8_2006:      2006      y
212_16_2006:      2006      y
196_1_2004:      2004      y

CPU time taken: 0 seconds.

*-----------------------------------------------------------*
RESULTS WITHOUT THE CLOCK:
Log Likelihood = -979.601279953959;
Shared Parameters:
R=1

Tree givenTree=(((((199_23_2006:0.000788578,199_26_2006:0.00158065)Node4:1.83076e-07,
212_15_2006:0.000788715)Node3:3.6469e-07,(211_13_2006:0.000789429,15_118_1995:7.
43913e-31)Node8:7.43913e-31)Node2:7.43913e-31,(211_32_2004:7.43913e-31,(196_13_2
006:0.00118462,212_8_2006:0.00118462)Node13:0.000395601)Node11:1.03077e-06)Node1
:7.43913e-31,212_16_2006:0.00158193,196_1_2004:0.00237528);
*-----------------------------------------------------------*

RESULTS WITH DATED TIPS CLOCK:
Log-likelihood: -976.156867934826
CPU time taken: 0.172 seconds.

*-----------------------------------------------------------*

-2(Ln Likelihood Ratio)=-6.88882
Constrained parameters:8
Asymptotic p-value:1
Tree with branch lengths scaled in y:
(((((199_23_2006:937.422,199_26_2006:937.422):0,212_15_2006:937.422):0,(211_13_2
006:702.769,15_118_1995:691.769):234.652):0,(211_32_2004:935.422,(196_13_2006:93
7.422,212_8_2006:937.422):0):0):242.507,212_16_2006:1179.93,196_1_2004:1177.93)

Root of the tree placed at 826.072(95% CI: 220.571,1248.19) y

Substitution rate estimated at 2.25987e-06(95% CI: 0.0012726,0.00366052) subs per y per site
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Sergei
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Datamonkeys are forever...

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Re: bugzilla and datedtipmolecularclock.bf
Reply #1 - Feb 7th, 2007 at 11:55am
 
Dear Gustavo,

Bugzilla: our sendmail seems to be eating the messages (I'll fix it ASAP)

DatedtipsMolecularClock.bf: Delete
Code:
MAXIMUM_ITERATIONS_PER_VARIABLE = smipv;
 


from the end of the file (TemplateBatchFiles/DatedtipsMolecularClock.bf) and all should be well. Thanks for pointing this bug out!

Cheers,
Sergei
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