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bali-phy-users

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Roni L, Benjamin Redelings6

Mar 20

Removed sequences

Hi Ben, Apologies, I am studying part time hence the spaced out responses. Re-adding C20 models (with

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Removed sequences

Hi Ben, Apologies, I am studying part time hence the spaced out responses. Re-adding C20 models (with

Mar 20

Roni L, Benjamin Redelings13

11/29/24

OK, I replaced the file bali-phy-4.0-beta16-win64.tar.gz with a new version that fixes some problems

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OK, I replaced the file bali-phy-4.0-beta16-win64.tar.gz with a new version that fixes some problems

11/29/24

Ziad Khouri, Benjamin Redelings4

9/6/24

Topology constraints possible?

Hi Ben, Thank you for getting back to me and apologies for the late response. The use case I was

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Topology constraints possible?

Hi Ben, Thank you for getting back to me and apologies for the late response. The use case I was

9/6/24

Cristian Sharma

10/6/23

Bali-Phy bp-analyze bug report

Hi Ben, I am using bp-analyze to check if my runs have converged by running it as so: bp-analyze run-

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Bali-Phy bp-analyze bug report

Hi Ben, I am using bp-analyze to check if my runs have converged by running it as so: bp-analyze run-

10/6/23

Pascal Title, Benjamin Redelings7

9/22/23

Error in bp-analyze

That's actually fine. I'll probably hide that message in the next release. It just means that

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Error in bp-analyze

That's actually fine. I'll probably hide that message in the next release. It just means that

9/22/23

Cedric Chauve, Benjamin Redelings2

3/27/23

Bug report: substitution model

Hi Cedric, I checked that this command works on the binaries of 4.0-beta2 released on github. Did you

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Bug report: substitution model

Hi Cedric, I checked that this command works on the binaries of 4.0-beta2 released on github. Did you

3/27/23

Marc Hömberger, … mmi...@sdsc.edu9

9/20/22

Possibility for checkpoint?

Hi Ben, We can't use Docker at present, due to security concerns on our HPC machine. However, I

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Possibility for checkpoint?

Hi Ben, We can't use Docker at present, due to security concerns on our HPC machine. However, I

9/20/22

Wayne Pfeiffer, Benjamin Redelings3

7/12/22

Memory usage of 3.6.1 becomes much higher than that of 3.4.1 as the number of taxa increases

Hi Ben, Thanks for the prompt reply! Good luck on tracking down the increase in memory usage :) Wayne

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Memory usage of 3.6.1 becomes much higher than that of 3.4.1 as the number of taxa increases

Hi Ben, Thanks for the prompt reply! Good luck on tracking down the increase in memory usage :) Wayne

7/12/22

Benjamin Redelings

2/7/22

What are "indel groups" in "alignment-info"?

Hi, I was asked what "indel groups" means in the "alignment-info" program. Here

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What are "indel groups" in "alignment-info"?

Hi, I was asked what "indel groups" means in the "alignment-info" program. Here

2/7/22

Benjamin Redelings, Karolis Ramanauskas2

7/22/21

Documentation patches

PR created. Hopefully, I didn't mess up anything. I used a Mac (case-insensitive file system),

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Documentation patches

PR created. Hopefully, I didn't mess up anything. I used a Mac (case-insensitive file system),

7/22/21

Karolis Ramanauskas, Benjamin Redelings7

7/20/21

Different definitions of the posP parameter between the m2 and m8 models

Hi, Points #1 and #2 make sense and clarify the behavior of BAli-Phy. Regarding your question in #3

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Different definitions of the posP parameter between the m2 and m8 models

Hi, Points #1 and #2 make sense and clarify the behavior of BAli-Phy. Regarding your question in #3

7/20/21

Karolis Ramanauskas, Benjamin Redelings5

7/19/21

Correct usage of codon models with rate heterogeneity across sites and mX(a) models estimating omega.

Thank you, I fundamentally misunderstood m8/m8a models. This makes perfect sense. Karolis On Monday,

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Correct usage of codon models with rate heterogeneity across sites and mX(a) models estimating omega.

Thank you, I fundamentally misunderstood m8/m8a models. This makes perfect sense. Karolis On Monday,

7/19/21

Karolis Ramanauskas, Benjamin Redelings3

7/15/21

Do the consensus tree branch lengths need to be rescaled manually?

Thanks, Benjamin, Personally, just knowing that the branches should be rescaled by a partition-

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Do the consensus tree branch lengths need to be rescaled manually?

Thanks, Benjamin, Personally, just knowing that the branches should be rescaled by a partition-

7/15/21

朱鑫鑫, Benjamin Redelings2

6/21/21

Seeking help for ancestal sequence reconstruction with bali-phy-3.6.0

Hi 鑫鑫, Did you run bp-analyze? If so, did you look at the generated file "index.html" using

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Seeking help for ancestal sequence reconstruction with bali-phy-3.6.0

Hi 鑫鑫, Did you run bp-analyze? If so, did you look at the generated file "index.html" using

6/21/21

Aaron Lewis, Benjamin Redelings3

4/27/21

Paralogous partitions?

Hi, Ben, and thanks for the tips, particularly the suggestion to condition on the subtrees matching.

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Paralogous partitions?

Hi, Ben, and thanks for the tips, particularly the suggestion to condition on the subtrees matching.

4/27/21

bobbyr...@gmail.com, … Aaron Lewis6

4/6/21

Segmentation Fault

Thanks for the linuxbrew tip. As workarounds go, for anyone else that finds this: the seg fault was

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Segmentation Fault

Thanks for the linuxbrew tip. As workarounds go, for anyone else that finds this: the seg fault was

4/6/21

Douglas Theobald, Benjamin Redelings4

3/5/21

bp-analyze misbehavior

Hi Douglas, Interesting ... that's unfortunately that SVG is unavailable for some platforms! I

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bp-analyze misbehavior

Hi Douglas, Interesting ... that's unfortunately that SVG is unavailable for some platforms! I

3/5/21

Tyler Ruddenfort, Benjamin Redelings7

1/19/21

exit: -9 (Computing ancestral state alignement

Hi Tyler, Thank you for the files. It looks like creating the ancestral sequence alignment was both (

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exit: -9 (Computing ancestral state alignement

Hi Tyler, Thank you for the files. It looks like creating the ancestral sequence alignment was both (

1/19/21

Bobby Read, Benjamin Redelings6

9/23/20

P1.max FASTA file no longer being generated

Great! Its good to have these kinds of problems/solutions available on the mailing list archives. -

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P1.max FASTA file no longer being generated

Great! Its good to have these kinds of problems/solutions available on the mailing list archives. -

9/23/20

Maya Gupta, Benjamin Redelings4

8/3/20

Likelihood Score Question

Hi Maya, Oh, I see. I think I should refer you to the "Probabilistic Model" section of the

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Likelihood Score Question

Hi Maya, Oh, I see. I think I should refer you to the "Probabilistic Model" section of the

8/3/20

Vanantwerp, James, … James Van Antwerp3

7/26/20

Multiple Substitution Matrices for Transmembrane Proteins

That looks very helpful! I am new to using Bali-Phy, and will need to talk with my advisor about the

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Multiple Substitution Matrices for Transmembrane Proteins

That looks very helpful! I am new to using Bali-Phy, and will need to talk with my advisor about the

7/26/20

Benjamin Redelings

7/6/20

New version 3.5.0.2 - compilation fix only

Hi everyone, In case anyone has had trouble compiling version 3.5.0 from source, I've released

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New version 3.5.0.2 - compilation fix only

Hi everyone, In case anyone has had trouble compiling version 3.5.0 from source, I've released

7/6/20

Leonid Rusin, Benjamin Redelings2

6/24/20

bp-analyze (logging.debug)

Thanks for the report! I'm going to follow this up on the issue that you filed. -BenRI On 6/24/20

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bp-analyze (logging.debug)

Thanks for the report! I'm going to follow this up on the issue that you filed. -BenRI On 6/24/20

6/24/20

Benjamin Redelings

6/19/20

Re: Bali-Phy Question

Hi Ben, BTW, would you mind sending questions to the google group, so that other people can benefit

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Re: Bali-Phy Question

Hi Ben, BTW, would you mind sending questions to the google group, so that other people can benefit

6/19/20

samuel.e....@gmail.com, Benjamin Redelings4

6/1/20

jointly estimating the alignment and presence of positive-selection with bali-phy

I guess I should point out that if you use a site model, such as m8a, then the tree and the alignment

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jointly estimating the alignment and presence of positive-selection with bali-phy

I guess I should point out that if you use a site model, such as m8a, then the tree and the alignment

6/1/20

W. Yin, Benjamin Redelings3

6/1/20

Diagnostics using the Effective sample sizes (ESS) and Stabilisation

Dear BenRI, Thank you so much for your kind reply and very detailed explanation. Sorry for replying

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Diagnostics using the Effective sample sizes (ESS) and Stabilisation

Dear BenRI, Thank you so much for your kind reply and very detailed explanation. Sorry for replying

6/1/20

Ben Read, … bobbyr...@gmail.com7

5/5/20

troubles with installation

Thank you, Ben! this has all worked perfectly and I can now visualise the results too in FigTree and

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troubles with installation

Thank you, Ben! this has all worked perfectly and I can now visualise the results too in FigTree and

5/5/20

Maya Gupta, Benjamin Redelings3

4/21/20

Linking BAli-Phy to local copy of GLIBC

Just re-downloaded it onto the cluster - it works now! Thank you!! On Monday, April 20, 2020 at 2:29:

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Linking BAli-Phy to local copy of GLIBC

Just re-downloaded it onto the cluster - it works now! Thank you!! On Monday, April 20, 2020 at 2:29:

4/21/20

Michael Sennett, Benjamin Redelings2

11/15/19

Trees contain a single taxa at a node

Hi Michael, Thanks for the bug report! 1. Just to make sure I'm understanding you correctly, are

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Trees contain a single taxa at a node

Hi Michael, Thanks for the bug report! 1. Just to make sure I'm understanding you correctly, are

11/15/19

彭婷, Benjamin Redelings2

9/30/19

Problems with the tree format of MAP tree

Hi Cynthia, I think the problem is that the root is placed on a leaf node. I will try and fix this

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Problems with the tree format of MAP tree

Hi Cynthia, I think the problem is that the root is placed on a leaf node. I will try and fix this

9/30/19

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