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Stepan Puhov
,
Benoit Morel
3
Apr 19
GeneRax: Support for site-specific frequency profiles
Dear Benoit, Well, for me it's a pity to learn about your leaving academia, but I would like to
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GeneRax: Support for site-specific frequency profiles
Dear Benoit, Well, for me it's a pity to learn about your leaving academia, but I would like to
Apr 19
Brenda Delamonica
,
Benoit Morel
2
Mar 28
Issue compiling AleRax
Hi Brenda, It seems to be an issue with one dependency of AleRax. I'm not quite sure that it will
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Issue compiling AleRax
Hi Brenda, It seems to be an issue with one dependency of AleRax. I'm not quite sure that it will
Mar 28
Hongyue Liu
,
Benoit Morel
4
Mar 2
AleRax: Error, the fraction of missing file does not cover the species 4
Hi Mia, Please try to replace the semi-columns with spaces. I think it should fix the problem. Sorry
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AleRax: Error, the fraction of missing file does not cover the species 4
Hi Mia, Please try to replace the semi-columns with spaces. I think it should fix the problem. Sorry
Mar 2
Jan Hackel
,
Benoit Morel
8
Feb 20
Node numbering for plotting results
Hi Benoit, OK I see. In my case, I used gene trees estimated separately. I think it would be great if
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Node numbering for plotting results
Hi Benoit, OK I see. In my case, I used gene trees estimated separately. I think it would be great if
Feb 20
Alejandro Gil-Gómez
,
Benoit Morel
10
Feb 9
Transfers to the past
Thank you so much for all the help! Libre de virus.www.avg.com El vie, 9 feb 2024 a las 5:33, Benoit
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Transfers to the past
Thank you so much for all the help! Libre de virus.www.avg.com El vie, 9 feb 2024 a las 5:33, Benoit
Feb 9
Alan Beavan
,
Benoit Morel
4
Feb 7
Issue with large supplied species tree
No problem, thanks for the feedback. I'll see if I can output a more explicit error message when
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Issue with large supplied species tree
No problem, thanks for the feedback. I'll see if I can output a more explicit error message when
Feb 7
Alan Beavan
Feb 7
generax failing with large given species tree
Hi Benoit, I wondered if you'd be able to help me. I am trying to run gene rax on some multiple
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generax failing with large given species tree
Hi Benoit, I wondered if you'd be able to help me. I am trying to run gene rax on some multiple
Feb 7
Stepan Puhov
,
Benoit Morel
4
Feb 2
AleRax fraction-missing option usage
We haven't benchmarked the different solutions. The pruned mode was initially implemented for
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AleRax fraction-missing option usage
We haven't benchmarked the different solutions. The pruned mode was initially implemented for
Feb 2
Ferdinand Marlétaz
,
Benoit Morel
3
Jan 30
Species tree rooted
Thanks a lot, got it! On Thu, Jan 25 2024 at 9:13 am, Benoit Morel <beno...@gmail.com> wrote:
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Species tree rooted
Thanks a lot, got it! On Thu, Jan 25 2024 at 9:13 am, Benoit Morel <beno...@gmail.com> wrote:
Jan 30
Stepan Puhov
,
Benoit Morel
18
Jan 26
AleRax bugs and requests
I didn't have the time to look at these yet. But I just fixed 1) (hopefully). The branch lengths
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AleRax bugs and requests
I didn't have the time to look at these yet. But I just fixed 1) (hopefully). The branch lengths
Jan 26
Alexandros Stamatakis
Jan 16
Crete May 2024 - Machine Learning for Evolutionary Genomics Data
Dear Users of our Software, Sorry for bothering you with some event advertisement again via this list
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Crete May 2024 - Machine Learning for Evolutionary Genomics Data
Dear Users of our Software, Sorry for bothering you with some event advertisement again via this list
Jan 16
杨宇航
,
Benoit Morel
4
12/23/23
Can Not Initialize ccps and evaluators
Hi Yohan, Maybe one thing you could try is to identify if specific families that are causing the
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Can Not Initialize ccps and evaluators
Hi Yohan, Maybe one thing you could try is to identify if specific families that are causing the
12/23/23
Alessandra Aleotti
,
Benoit Morel
3
12/12/23
List of all modules allowed with correct syntax
Hi Benoit, Thanks a lot, that's exactly what I was looking for! Best, Alessandra On Tue, 12 Dec
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List of all modules allowed with correct syntax
Hi Benoit, Thanks a lot, that's exactly what I was looking for! Best, Alessandra On Tue, 12 Dec
12/12/23
Wen-Cong Huang
11/22/23
Alerax: DTL rates of different lineages stuck at 0.1,0.1,0.1 after rate optimisation
Hi Benoit, I tried to reconcille gene family trees against different species trees, by allowing
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Alerax: DTL rates of different lineages stuck at 0.1,0.1,0.1 after rate optimisation
Hi Benoit, I tried to reconcille gene family trees against different species trees, by allowing
11/22/23
Alexandros Stamatakis
11/15/23
Two weeks remaining to apply for 2024 Summer School on Computational Molecular Evolution
Dear Users of our software tools, The deadline for applications to our 14th summer school on
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Two weeks remaining to apply for 2024 Summer School on Computational Molecular Evolution
Dear Users of our software tools, The deadline for applications to our 14th summer school on
11/15/23
John Soghigian
,
Benoit Morel
5
11/2/23
Invalid gene family
That did it! Thanks, Benoit :) John On Thu, Nov 2, 2023 at 8:45 AM Benoit Morel <benomorel@gmail.
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Invalid gene family
That did it! Thanks, Benoit :) John On Thu, Nov 2, 2023 at 8:45 AM Benoit Morel <benomorel@gmail.
11/2/23
Alexandros Stamatakis
10/26/23
Applications for 2024 Summer School on Computational Molecular Evolution are open
Dear Users of our software tools, The applications for our 14th summer school on COmputational
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Applications for 2024 Summer School on Computational Molecular Evolution are open
Dear Users of our software tools, The applications for our 14th summer school on COmputational
10/26/23
Stepan Puhov
,
Benoit Morel
5
10/25/23
Joint LL decreases during gene tree optimization
1. Well, I am not sure that I quite understand. If you re-optimize the libpll model from scratch at
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Joint LL decreases during gene tree optimization
1. Well, I am not sure that I quite understand. If you re-optimize the libpll model from scratch at
10/25/23
Stepan Puhov
,
Benoit Morel
6
10/10/23
LG4X model compatibility
Dear Benoit, Great thanks! I'm really happy and profoundly grateful that you've managed to do
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LG4X model compatibility
Dear Benoit, Great thanks! I'm really happy and profoundly grateful that you've managed to do
10/10/23
Ben Woodcroft
,
Benoit Morel
2
8/24/23
SpeciesRax resumable?
Hi Ben, No it can't be resumed. What you suggest is a good idea. I think you will still waste
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SpeciesRax resumable?
Hi Ben, No it can't be resumed. What you suggest is a good idea. I think you will still waste
8/24/23
Alexandros Stamatakis
7/11/23
One PostDoc Positions in my new research group in Crete
Dear Users of our Software, Please accept my apologies that I am slightly misusing our software
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One PostDoc Positions in my new research group in Crete
Dear Users of our Software, Please accept my apologies that I am slightly misusing our software
7/11/23
Yoann Pellen
,
Benoit Morel
3
5/30/23
Look for gene tree branches in specific species tree branch
Thanks a lot! I did try thirdkind but since I'll have thousands of sequences to check I need a
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Look for gene tree branches in specific species tree branch
Thanks a lot! I did try thirdkind but since I'll have thousands of sequences to check I need a
5/30/23
Dinko Novosel
,
Benoit Morel
12
5/27/23
mapping.link
Hi Benoit! I solve problem even I still don't know what real problem was. All files were ok
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mapping.link
Hi Benoit! I solve problem even I still don't know what real problem was. All files were ok
5/27/23
冯晓远
,
Benoit Morel
3
5/23/23
Understanding reconciliated gene trees
Dear Benoit, Thank you for your prompt response! It helps me a lot. My dataset does contain frequent
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Understanding reconciliated gene trees
Dear Benoit, Thank you for your prompt response! It helps me a lot. My dataset does contain frequent
5/23/23
Sawsan Wehbi
,
Benoit Morel
2
5/12/23
DTL rates
Hi Sawsan, I think the DTL rates should be estimated by default in both modes, but I can double-check
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DTL rates
Hi Sawsan, I think the DTL rates should be estimated by default in both modes, but I can double-check
5/12/23
Bo Feng
,
Benoit Morel
7
4/25/23
Run error: Aborted (core dumped)
Great ;-) Yes, viewing large trees is really problematic, I hope that someday someone will have a
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Run error: Aborted (core dumped)
Great ;-) Yes, viewing large trees is really problematic, I hope that someday someone will have a
4/25/23
Sawsan Wehbi
,
Benoit Morel
4
4/20/23
Costume substitution model
Update: in fact, apparently, we already support the non reversible Q matrices inferred from the pfam
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Costume substitution model
Update: in fact, apparently, we already support the non reversible Q matrices inferred from the pfam
4/20/23
Jan Hackel
,
Benoit Morel
3
4/14/23
Memory requirements and memory distribution
Hi Jan, Thanks for your feedback. You're right, I'll add a paragraph about memory
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Memory requirements and memory distribution
Hi Jan, Thanks for your feedback. You're right, I'll add a paragraph about memory
4/14/23
Sawsan Wehbi
,
Benoit Morel
2
3/21/23
Generax checkpoints
Dear Sawsan, To use checkpointing, you only need to restart GeneRax with the exact same command. It
unread,
Generax checkpoints
Dear Sawsan, To use checkpointing, you only need to restart GeneRax with the exact same command. It
3/21/23
Sawsan Wehbi
,
Benoit Morel
2
3/4/23
Selenocysteine might be preventing generax from reading alignment files
Dear Sawsan Wehbi, I can check next week, but yes, that's likely the right explanation. If you
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Selenocysteine might be preventing generax from reading alignment files
Dear Sawsan Wehbi, I can check next week, but yes, that's likely the right explanation. If you
3/4/23