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Hilbert Heisenberg
9/6/20
Testnh | ParameterException: ConstraintException: ParameterList::matchParametersValues
Hi, I tried to prove the non-homogeneity with Testnh of a new model with parameters estimated by
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Testnh | ParameterException: ConstraintException: ParameterList::matchParametersValues
Hi, I tried to prove the non-homogeneity with Testnh of a new model with parameters estimated by
9/6/20
Shea Lambert
8/23/16
Q&A
Substitution mapping
Hello, I'd like to use bppml and testNH to replicate the substitution mapping procedure of
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Q&A
Substitution mapping
Hello, I'd like to use bppml and testNH to replicate the substitution mapping procedure of
8/23/16
Shea Lambert
,
Julien Yann Dutheil
2
8/23/16
Q&A
Version 1.1.0
Dear Shea, Indeed, thanks a lot for reporting this! Best regards, Julien.
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Q&A
Version 1.1.0
Dear Shea, Indeed, thanks a lot for reporting this! Best regards, Julien.
8/23/16
Benoit NABHOLZ
,
Julien Yann Dutheil
3
9/15/15
Q&A
Can't execute pre-compiled executable
Should be fixed now :) J.
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Q&A
Can't execute pre-compiled executable
Should be fixed now :) J.
9/15/15
Tristan Lefebure
, …
Florent Lassalle
29
8/28/14
testNH vs gabranch
I must add that GAbrach is actually no more supported in HyPhy, because they say that their
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testNH vs gabranch
I must add that GAbrach is actually no more supported in HyPhy, because they say that their
8/28/14
Julien Yann Dutheil
,
Laurent Guéguen
2
6/10/14
Re: mapnh-counts/rates
Dear Paulina & Julien, yes indeed, the usual output of mapnh does not normalize the counts, so
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Re: mapnh-counts/rates
Dear Paulina & Julien, yes indeed, the usual output of mapnh does not normalize the counts, so
6/10/14
Pau Bolivar
,
Julien Yann Dutheil
3
6/3/14
Compile Error
Thanks a lot!! Now it worked!! Cheers! Paulina
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Compile Error
Thanks a lot!! Now it worked!! Cheers! Paulina
6/3/14
Fidel Botero
,
Julien Yann Dutheil
3
9/20/13
Counts in mapNH, option All
Great ! Thanks a lot, Julien ! Le lundi 9 septembre 2013 15:05:42 UTC+2, Fidel Botero a écrit : Hello
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Counts in mapNH, option All
Great ! Thanks a lot, Julien ! Le lundi 9 septembre 2013 15:05:42 UTC+2, Fidel Botero a écrit : Hello
9/20/13
Glémin Sylvain
, …
Bastien Boussau
8
8/30/13
problem with tree root
OK Many thanks Sylvain On Thursday, August 29, 2013 9:54:07 PM UTC+2, Glémin Sylvain wrote: Hello, I
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problem with tree root
OK Many thanks Sylvain On Thursday, August 29, 2013 9:54:07 PM UTC+2, Glémin Sylvain wrote: Hello, I
8/30/13
Benoit NABHOLZ
,
Julien Yann Dutheil
2
5/2/13
Compatibility testNH and bio++ 2.1
Hi Benoit, TestNH has not yet been updated to the newest version of Bio++. I mean, the packages are
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Compatibility testNH and bio++ 2.1
Hi Benoit, TestNH has not yet been updated to the newest version of Bio++. I mean, the packages are
5/2/13
alex
,
Julien Yann Dutheil
6
1/9/13
Q&A
codon models
Dear Julies, Thanks! Yes, I use MapNH. I try to use useObservedFreqs=yes as in the examples, but the
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Q&A
codon models
Dear Julies, Thanks! Yes, I use MapNH. I try to use useObservedFreqs=yes as in the examples, but the
1/9/13
alex
12/13/12
Q&A
Branch-site model?
Hello! I just discover testnh and I would like to use it for Substitution mapping. Is it possible to
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Q&A
Branch-site model?
Hello! I just discover testnh and I would like to use it for Substitution mapping. Is it possible to
12/13/12
Tristan Lefebure
,
Julien Yann Dutheil
2
11/29/12
mapNH, types and counts
Hi Tristan, A good old issue... we really need to document that.1 is synonymous, 2 is nonsynonymous.
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mapNH, types and counts
Hi Tristan, A good old issue... we really need to document that.1 is synonymous, 2 is nonsynonymous.
11/29/12
Claudia Weber
,
Julien Yann Dutheil
3
10/17/12
Conservative vs non-conservative substitutions
Dear Julien, Thanks for the quick response! Yes, I think that a flexible solution similar to the
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Conservative vs non-conservative substitutions
Dear Julien, Thanks for the quick response! Yes, I think that a flexible solution similar to the
10/17/12
Tristan Lefebure
, …
Laurent Guéguen
4
9/30/12
Stop codon
Hi Tristan, in the usual codon models, indeed stop codons are not considered, perhaps because it is
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Stop codon
Hi Tristan, in the usual codon models, indeed stop codons are not considered, perhaps because it is
9/30/12
Laurent Guéguen
, …
Julien Yann Dutheil
25
9/28/12
missing model for a branch ?
Ok. See previous email for the compilation issue. J. On Fri, Sep 28, 2012 at 5:19 PM, Tristan
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missing model for a branch ?
Ok. See previous email for the compilation issue. J. On Fri, Sep 28, 2012 at 5:19 PM, Tristan
9/28/12
Giap Nguyen
,
Julien Yann Dutheil
2
9/13/12
About initial length of input tree in TestNH
Hi Nguyen, For the branch lengths units, Laurent can answer better than me. In any case, this does
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About initial length of input tree in TestNH
Hi Nguyen, For the branch lengths units, Laurent can answer better than me. In any case, this does
9/13/12
Giap Nguyen
,
Julien Yann Dutheil
2
9/2/12
omega value from N & S counts
Hi, In this R script, I simply copy the tree.S into tree.dNdS, and then change the branch lengths to
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omega value from N & S counts
Hi, In this R script, I simply copy the tree.S into tree.dNdS, and then change the branch lengths to
9/2/12
Giap Nguyen
,
Julien Yann Dutheil
2
9/2/12
Is it a limitation of TestNH?
Hi Nguyen, The "auto" clustering is for when Dn and Ds are two small. It is not that they
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Is it a limitation of TestNH?
Hi Nguyen, The "auto" clustering is for when Dn and Ds are two small. It is not that they
9/2/12
nvgiap
,
Julien Yann Dutheil
10
8/30/12
Is it an incongruent in result?
Hi Nguyen, Finally solved that bug, which occurred only when the homogenous model (1 partition) was
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Is it an incongruent in result?
Hi Nguyen, Finally solved that bug, which occurred only when the homogenous model (1 partition) was
8/30/12
Tristan Lefebure
, …
Julien Yann Dutheil
5
8/30/12
Q&A
very large omega values
Hi, Indeed. One can also use Marginal(threshold=1), to ensure all categories are represented. In
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Q&A
very large omega values
Hi, Indeed. One can also use Marginal(threshold=1), to ensure all categories are represented. In
8/30/12
Laurent Guéguen
,
Julien Yann Dutheil
8
7/13/12
non stationarity for codon models
Even in this case it is not so easy to make categories, because a codon is not only more of GCs or
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non stationarity for codon models
Even in this case it is not so easy to make categories, because a codon is not only more of GCs or
7/13/12
Laurent Guéguen
,
Julien Yann Dutheil
3
7/11/12
data for examples
Yes, but I found the .phy file in Mantellid. L On 11 juil, 13:52, Julien Yann Dutheil <jy.duth...@
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data for examples
Yes, but I found the .phy file in Mantellid. L On 11 juil, 13:52, Julien Yann Dutheil <jy.duth...@
7/11/12
Laurent Guéguen
,
Julien Yann Dutheil
2
7/11/12
output of mapnh
Hi Laurent, That comes from the SubstitutionRegister class, but it is true that we should output this
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output of mapnh
Hi Laurent, That comes from the SubstitutionRegister class, but it is true that we should output this
7/11/12
nvgiap
,
Julien Yann Dutheil
2
7/11/12
Understanding PartNH results
Dear Nguyen, > 1. I get confusing in choosing what is the best partion from the following >
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Understanding PartNH results
Dear Nguyen, > 1. I get confusing in choosing what is the best partion from the following >
7/11/12
Tristan Lefebure
,
Julien Yann Dutheil
2
7/10/12
mapnh, count.max
Hi Tristan, It is the maximum number of counts on a branch-site, to control for saturation. It is
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mapnh, count.max
Hi Tristan, It is the maximum number of counts on a branch-site, to control for saturation. It is
7/10/12