dppdiv-users

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Welcome to the DPPDiv user group. Please feel free to post questions about analysis, installation, models, etc. More information about this program can be found here: http://phylo.bio.ku.edu/content/tracy-heath-dppdiv.

Cheers!

Tracy

0 selected

mmi...@sdsc.edu, … Mark Derbyshire12

3/12/20

questions about a few command lines

Hi Tracy, Have you put together that manual yet? It's 7 years since this thread was started.

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questions about a few command lines

Hi Tracy, Have you put together that manual yet? It's 7 years since this thread was started.

3/12/20

Mark Derbyshire

2/28/20

dppdiv-par-sse: MbRandom.cpp:1742: unsigned int MbRandom::categoricalRv(const double*, unsigned int): Assertion `u < 1.0e-6' failed.

Dear dppdiv users and developers, I'm currently trying to run dppdiv-par on a large concatenated

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dppdiv-par-sse: MbRandom.cpp:1742: unsigned int MbRandom::categoricalRv(const double*, unsigned int): Assertion `u < 1.0e-6' failed.

Dear dppdiv users and developers, I'm currently trying to run dppdiv-par on a large concatenated

2/28/20

Alexandros Stamatakis

10/31/19

Application deadline (NOV 18) Summer School on Computational Molecular Evolution Crete 2020 approaching

Dear Users of our Software, Applications for our 12th summer school on computational molecular

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Application deadline (NOV 18) Summer School on Computational Molecular Evolution Crete 2020 approaching

Dear Users of our Software, Applications for our 12th summer school on computational molecular

10/31/19

Chloe Tan, … Tomas Flouri5

3/19/19

Error while running DPPDIV on CIPRES

Hi Tomas, I've tried that, this is what the tree looks like: ((((ATCC29927:0.00301571,(CITHA-6:

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Error while running DPPDIV on CIPRES

Hi Tomas, I've tried that, this is what the tree looks like: ((((ATCC29927:0.00301571,(CITHA-6:

3/19/19

alexandre pedro, … Stephanie Loria17

9/10/18

Segmentation Fault Problem

Hi All, I am having the same problem as everyone else. Cipres is terminating the same way. Best

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Segmentation Fault Problem

Hi All, I am having the same problem as everyone else. Cipres is terminating the same way. Best

9/10/18

Alexandros Stamatakis

8/11/17

10th Summer School on Computational Molecular Evolution

Dear Software Users, Applications for the 10th summer school on computational molecular evolution in

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10th Summer School on Computational Molecular Evolution

Dear Software Users, Applications for the 10th summer school on computational molecular evolution in

8/11/17

yinghu...@gmail.com

3/22/17

DPPDiv stuck when use FBD model

Dear all, When I use the FBD model of FDPPDIV-1.3 to analyse my data, it is stuck. One week passed,

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DPPDiv stuck when use FBD model

Dear all, When I use the FBD model of FDPPDIV-1.3 to analyse my data, it is stuck. One week passed,

3/22/17

Alison Ravenscraft, Tracy Heath2

1/5/17

generating an ultrametric tree from a non-ultrametric tree?

Hi Alison, Sorry for the slow response. You can estimate relative branch times in DPPDiv and most

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generating an ultrametric tree from a non-ultrametric tree?

Hi Alison, Sorry for the slow response. You can estimate relative branch times in DPPDiv and most

1/5/17

Olivier De Clerck, Tracy Heath2

1/5/17

Hi Olivier, Sorry for the slow response, your email got buried. From your email, I take it that you

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Hi Olivier, Sorry for the slow response, your email got buried. From your email, I take it that you

1/5/17

Alexandros Stamatakis

9/15/16

9th summer school on computational molecular evolution May 8 - 19, Hinxton, UK

Dear Users and former Course Participants, The 9th summer school on computational molecular evolution

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9th summer school on computational molecular evolution May 8 - 19, Hinxton, UK

Dear Users and former Course Participants, The 9th summer school on computational molecular evolution

9/15/16

Mark Miller, Tracy Heath5

8/8/16

troubles with file format

Yeah, thanks Tracy. I had a doubt as to whether the issue might be the flag, and not actually line

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troubles with file format

Yeah, thanks Tracy. I had a doubt as to whether the issue might be the flag, and not actually line

8/8/16

Alexandros Stamatakis3

10/20/15

8th summer school on computational molecular evolution in Crete

Dear Users, This is the last reminder, the strict deadline for submitting applications is in 10 days

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8th summer school on computational molecular evolution in Crete

Dear Users, This is the last reminder, the strict deadline for submitting applications is in 10 days

10/20/15

sah...@iisertvm.ac.in, Tracy Heath4

9/27/15

FDPPDIV-fossil calibration&more

Hi Ranjit, For any analysis using fossils, it is ideal to assign them as precisely as possible. You

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FDPPDIV-fossil calibration&more

Hi Ranjit, For any analysis using fossils, it is ideal to assign them as precisely as possible. You

9/27/15

alexandre pedro, … Tracy Heath10

8/31/15

Calibration file

Hi Liang, This depends very much on your application of calibration priors or fossil taxa (if you

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Calibration file

Hi Liang, This depends very much on your application of calibration priors or fossil taxa (if you

8/31/15

Li Wang, … Deren Eaton11

7/10/15

error concerning dppdiv-pthreads-sse3

Hey everyone, I ran into this same problem recenly. I think it is a bug with parsing the newick

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error concerning dppdiv-pthreads-sse3

Hey everyone, I ran into this same problem recenly. I think it is a bug with parsing the newick

7/10/15

alexandre pedro, … Mark Miller4

5/26/15

Convergence and ESS values with DPPDIV

Hi all, I wanted to check and see if the FBD-DPPDIV is available in FDPPDIV code yet? For CIPRES to

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Convergence and ESS values with DPPDIV

Hi all, I wanted to check and see if the FBD-DPPDIV is available in FDPPDIV code yet? For CIPRES to

5/26/15

Shea Lambert, Tracy Heath3

4/2/15

ERROR: Problem adding a tip to the tree

Hi Tracy, It does turn out that the tree was not fully bifurcating. Fixed with multi2di() of R's

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ERROR: Problem adding a tip to the tree

Hi Tracy, It does turn out that the tree was not fully bifurcating. Fixed with multi2di() of R's

4/2/15

Nick L., Tracy Heath3

1/14/15

Substitution Rates

Thanks Tracy. On Tuesday, January 13, 2015 at 4:11:38 PM UTC, Tracy Heath wrote: For each tree

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Substitution Rates

Thanks Tracy. On Tuesday, January 13, 2015 at 4:11:38 PM UTC, Tracy Heath wrote: For each tree

1/14/15

Satoshi Eguchi, … Tracy Heath5

12/3/14

Failure to compile multi-thread version of FDPPDiv

Hi Tracy, My data contains 120 taxa. Thanks, Satoshi

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Failure to compile multi-thread version of FDPPDiv

Hi Tracy, My data contains 120 taxa. Thanks, Satoshi

12/3/14

Alejandro Zuluaga, Tracy Heath2

10/24/14

calibration file

Hi Alejandro, The -t flag indicates that the time provided represents a fossil occurrence time and

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calibration file

Hi Alejandro, The -t flag indicates that the time provided represents a fossil occurrence time and

10/24/14

Alejandro Zuluaga, Miller, Mark2

10/23/14

FDDDPDiv in Cipres

Hi Alejandro, It is not implemented at present, and we have not as of today received any requests for

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FDDDPDiv in Cipres

Hi Alejandro, It is not implemented at present, and we have not as of today received any requests for

10/23/14

Sebastian Duchene, Tracy Heath3

9/22/14

Tip-calibrations in DDPdiv

Hello Tracy, Thanks for your reply. I am actually interested in testing the DPP for those data. I

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Tip-calibrations in DDPdiv

Hello Tracy, Thanks for your reply. I am actually interested in testing the DPP for those data. I

9/22/14

Xin Chen, … Tracy Heath4

9/17/14

comparing results with different -pm of DPP priors and -urg prior

Hi Luis, It's nice to hear from you. The only sequence model available in DPPDiv is GTR+G, so

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comparing results with different -pm of DPP priors and -urg prior

Hi Luis, It's nice to hear from you. The only sequence model available in DPPDiv is GTR+G, so

9/17/14

Fabien Condamine, Tracy Heath2

8/1/14

Trouble to compile DPPDIV: error with the omp.h file

Hi Fabien, It seems like your gcc install didn't include omp.h or it is in the wrong place. If

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Trouble to compile DPPDIV: error with the omp.h file

Hi Fabien, It seems like your gcc install didn't include omp.h or it is in the wrong place. If

8/1/14

Nitish Narula, Tracy Heath3

7/25/14

Site Models for FBD analysis

Thanks for the reply, Tracy. I did get in touch with Sasha and Alexei about their plugin for BEAST2.

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Site Models for FBD analysis

Thanks for the reply, Tracy. I did get in touch with Sasha and Alexei about their plugin for BEAST2.

7/25/14

Xin Chen, Tracy Heath3

7/10/14

problem of compiling, thank you!

Thanks! On Thursday, July 10, 2014 5:16:22 PM UTC-4, Tracy Heath wrote: These errors seem to be

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problem of compiling, thank you!

Thanks! On Thursday, July 10, 2014 5:16:22 PM UTC-4, Tracy Heath wrote: These errors seem to be

7/10/14

Davide, … Tracy Heath4

5/26/14

recently diverged bacterial dataset

Dear Alexis and Tracy, thank you for your quick and informative replies. So I guess I'll have to

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recently diverged bacterial dataset

Dear Alexis and Tracy, thank you for your quick and informative replies. So I guess I'll have to

5/26/14

Teofil Nakov, … Tracy Heath6

12/19/13

pll dppdiv stuck or really slow ?

Yep, I noticed that too. Seems an unnecessary ping to the group. Happy holidays! On Thu, Dec 19, 2013

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pll dppdiv stuck or really slow ?

Yep, I noticed that too. Seems an unnecessary ping to the group. Happy holidays! On Thu, Dec 19, 2013

12/19/13

Matthew Olson, Tracy Heath2

10/9/13

Which version is the most up to date?

Hi Matt, This is a good question. The versions that Diego Darriba, Tomas Flouri, and Alexis

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Which version is the most up to date?

Hi Matt, This is a good question. The versions that Diego Darriba, Tomas Flouri, and Alexis

10/9/13

Nick L., Tracy Heath3

8/16/13

New results vs. Past results

Thanks so much, Tracy. On Saturday, August 3, 2013 2:23:02 PM UTC+1, Nick L. wrote: Dear Tracy, I

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New results vs. Past results

Thanks so much, Tracy. On Saturday, August 3, 2013 2:23:02 PM UTC+1, Nick L. wrote: Dear Tracy, I

8/16/13

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