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IQ-TREE
1–30 of 1859
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iqtree2/discussions
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Minh Bui
8/11/19
Re: [iqtree] IQ-TREE web server - does not work :(
Hi there, I believe this was due to a power outage, but only for a short duration. Cheers, Minh On 30
unread,
Answered
Re: [iqtree] IQ-TREE web server - does not work :(
Hi there, I believe this was due to a power outage, but only for a short duration. Cheers, Minh On 30
8/11/19
Eve
,
Minh Bui
4
8/16/19
Q&A
Question: Rate matrix Q with GTR+F+G4
Hi Eve again, Regarding your other questions: the diagonal elements are negative because sum of rows
unread,
Answered
Question
gamma
Q&A
Question: Rate matrix Q with GTR+F+G4
Hi Eve again, Regarding your other questions: the diagonal elements are negative because sum of rows
8/16/19
Dmitry Karabanov
,
Heiko Schmidt
3
7/30/19
Q&A
iqtree.cibiv.univie.ac.at - does not work
Thanks a lot! Oh, it was probably a problem with my file. My file's name had symbols ! and &
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Answered
Q&A
iqtree.cibiv.univie.ac.at - does not work
Thanks a lot! Oh, it was probably a problem with my file. My file's name had symbols ! and &
7/30/19
Zhifang Liu
,
Minh Bui
2
7/25/19
Q&A
how to update iqtree version in Linux
Hi Zhifang, See http://www.iqtree.org/doc/Quickstart#installation Cheers Minh On 25 Jul 2019, at 5:46
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Answered
Q&A
how to update iqtree version in Linux
Hi Zhifang, See http://www.iqtree.org/doc/Quickstart#installation Cheers Minh On 25 Jul 2019, at 5:46
7/25/19
Алсу Назипова
,
Minh Bui
3
7/24/19
Q&A
Which number of replicates for UltraFast bootstrap support I have to use to publish my tree in journal?
Thank you very much! среда, 24 июля 2019 г., 2:42:27 UTC+3 пользователь Minh Bui написал: Hi, The
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Answered
Q&A
Which number of replicates for UltraFast bootstrap support I have to use to publish my tree in journal?
Thank you very much! среда, 24 июля 2019 г., 2:42:27 UTC+3 пользователь Minh Bui написал: Hi, The
7/24/19
Carla Gonçalves
,
Minh Bui
4
7/16/19
Q&A
Determine Bootstrap support in given tree
Hi Minh, thank you, I think I just found the answer to my question in a previous thread: https://
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Answered
Q&A
Determine Bootstrap support in given tree
Hi Minh, thank you, I think I just found the answer to my question in a previous thread: https://
7/16/19
Wu
, …
Aline Silva
6
Jan 24
Q&A
ERROR: C:\Users\minh\Dropbox\iqtree-git\tree\phylotree.cpp:2652:
Hi, I'm trying to perform a maximum likelihood analysis IQTree, but after providing the
unread,
Answered
Q&A
ERROR: C:\Users\minh\Dropbox\iqtree-git\tree\phylotree.cpp:2652:
Hi, I'm trying to perform a maximum likelihood analysis IQTree, but after providing the
Jan 24
Bernardo Santos
, …
Minh Bui
4
7/14/19
Q&A
Combined morphological and molecular data
Sorry, to be more precise: this bug happens in the model selection step with these two options.
unread,
Answered
Q&A
Combined morphological and molecular data
Sorry, to be more precise: this bug happens in the model selection step with these two options.
7/14/19
Minh Bui
7/9/19
Re: [iqtree] Problem opening program
Hi Sariana, Please have a look at this quick guide for Windows: http://www.iqtree.org/doc/Quickstart#
unread,
Answered
Re: [iqtree] Problem opening program
Hi Sariana, Please have a look at this quick guide for Windows: http://www.iqtree.org/doc/Quickstart#
7/9/19
Brittany Rife Magalis
,
Minh Bui
2
7/10/19
Q&A
Prevent truncation of taxa names
Hi, There is no way to do that. When reading a FASTA file, IQ-TREE will discard parts of the sequence
unread,
Answered
Q&A
Prevent truncation of taxa names
Hi, There is no way to do that. When reading a FASTA file, IQ-TREE will discard parts of the sequence
7/10/19
Philipp Chetverikov
, …
张东
7
7/9/19
Q&A
mixture models and GUI
Hi Philipp, 1. At the time, we haven't included these functions in the PhyloSuite. 2. As IQ-TREE
unread,
Answered
Q&A
mixture models and GUI
Hi Philipp, 1. At the time, we haven't included these functions in the PhyloSuite. 2. As IQ-TREE
7/9/19
Zachary Griebenow
, …
Liu Jia
4
4/21/23
Q&A
Theoretical basis for bootstrap analysis "failure to converge"
Hello Minh, I am now using the IQTREE version 2.2.0, and also got the convergence issue (even with
unread,
Answered
Q&A
Theoretical basis for bootstrap analysis "failure to converge"
Hello Minh, I am now using the IQTREE version 2.2.0, and also got the convergence issue (even with
4/21/23
Eric Smidt
,
Minh Bui
3
7/1/19
Q&A
DNA partitions and morphology with polymorphism (12)
Hi Minh, yes, thanks a lot. I´m very happy with IQ-Tree All the best. Eric de Camargo Smidt Prof.
unread,
Answered
Q&A
DNA partitions and morphology with polymorphism (12)
Hi Minh, yes, thanks a lot. I´m very happy with IQ-Tree All the best. Eric de Camargo Smidt Prof.
7/1/19
张东
,
Minh Bui
3
6/30/19
Q&A
AU test query
Hi Minh, Thank you for your help. I am going to look into that book chapter. Sincerely, Dong Zhang 在
unread,
Answered
Q&A
AU test query
Hi Minh, Thank you for your help. I am going to look into that book chapter. Sincerely, Dong Zhang 在
6/30/19
YanYan
,
Minh Bui
5
7/2/19
Q&A
failed in modelfinder
Dear Minh: After adding -st DNA, IQ-tree works! Thank you! I am very happy that it is really fast.
unread,
Answered
Q&A
failed in modelfinder
Dear Minh: After adding -st DNA, IQ-tree works! Thank you! I am very happy that it is really fast.
7/2/19
Jessica
, …
IQ-TREE
3
6/30/19
Q&A
Could you share with the R code for the concord.cf.stat?
Hi Jessica, Minh is right. But if that's not working, here's the link: https://gist.github.
unread,
Answered
Q&A
Could you share with the R code for the concord.cf.stat?
Hi Jessica, Minh is right. But if that's not working, here's the link: https://gist.github.
6/30/19
Chih-Wei Huang
,
Minh Bui
3
6/25/19
Q&A
ERROR: Numerical underflow (lh-branch)
Hi Chih-Wei, Just as a head up: I saw that part1 has no invariant sites. This might or might not be
unread,
Answered
Q&A
ERROR: Numerical underflow (lh-branch)
Hi Chih-Wei, Just as a head up: I saw that part1 has no invariant sites. This might or might not be
6/25/19
Alexandros Vasilikopoulos
,
Minh Bui
3
6/26/19
Q&A
MULTISTATE MODEL FOR ANALYSES OF RECODED AMINO-ACID DATA
Many thanks Minh! On Tue, Jun 25, 2019 at 5:36 PM Minh Bui <minh...@univie.ac.at> wrote: Hi
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Answered
Q&A
MULTISTATE MODEL FOR ANALYSES OF RECODED AMINO-ACID DATA
Many thanks Minh! On Tue, Jun 25, 2019 at 5:36 PM Minh Bui <minh...@univie.ac.at> wrote: Hi
6/26/19
Jan Philip Oeyen
,
Minh Bui
2
6/25/19
Q&A
IQ-TREE 1.6.8: Data type detection problems (AA meta-partitions)
Hi Jan, This is part of the log file, where the detection might not print complete information. You
unread,
Answered
acids
amino
automatic
datatype
detection
meta-partitions
selection
Q&A
IQ-TREE 1.6.8: Data type detection problems (AA meta-partitions)
Hi Jan, This is part of the log file, where the detection might not print complete information. You
6/25/19
Michal Malszycki
,
Minh Bui
4
6/26/19
Q&A
Compare tree phylogenies calculated using different models
Ah ok, I didn't know that you have only one short gene. In that case, please do not use C20 or
unread,
Answered
MODEL
comparison
Q&A
Compare tree phylogenies calculated using different models
Ah ok, I didn't know that you have only one short gene. In that case, please do not use C20 or
6/26/19
Jacopo Martelossi
,
Minh Bui
3
6/25/19
Q&A
initial partitions influence on topology and branchlengths
Hi Minh, first of all thank's for your answer. I had already put some of your sugegstions in
unread,
Answered
Partition
Q&A
initial partitions influence on topology and branchlengths
Hi Minh, first of all thank's for your answer. I had already put some of your sugegstions in
6/25/19
Michel Domínguez Díaz
, …
Minh Bui
6
8/31/20
Q&A
binomial test of symetry
Hi Jake, I vaguely remember that someone else requested that feature. It's a valid request, we
unread,
Answered
Q&A
binomial test of symetry
Hi Jake, I vaguely remember that someone else requested that feature. It's a valid request, we
8/31/20
Diego Zhu
,
Minh Bui
4
6/12/19
Q&A
mix data with DNA sequences and binary data
Thank you very much Minh! I will have a go. On Wednesday, 12 June 2019 11:52:09 UTC+10, Minh Bui
unread,
Answered
Q&A
mix data with DNA sequences and binary data
Thank you very much Minh! I will have a go. On Wednesday, 12 June 2019 11:52:09 UTC+10, Minh Bui
6/12/19
Bruce Murphy
,
Minh Bui
2
5/31/19
re-running
Hi Bruce, This was answered: https://groups.google.com/forum/#!topic/iqtree/mA7-OIaHm9Y Fortunately,
unread,
Answered
re-running
Hi Bruce, This was answered: https://groups.google.com/forum/#!topic/iqtree/mA7-OIaHm9Y Fortunately,
5/31/19
Diego F. Morales-Briones
,
Minh Bui
3
6/2/19
Q&A
Output trees with missing taxa in partitioned analyses
Hi Diego, Now I see the problem: it's due to missing data. Your alignment has 11 sequences, but
unread,
Answered
Q&A
Output trees with missing taxa in partitioned analyses
Hi Diego, Now I see the problem: it's due to missing data. Your alignment has 11 sequences, but
6/2/19
张东
,
Stephen Crotty
5
5/28/19
Q&A
GHOST questions
Hi Stephen, I get it, thank you very much for your help. Sincerely, Dong 在 2019年5月28日星期二 UTC+8下午5:35:
unread,
Answered
Q&A
GHOST questions
Hi Stephen, I get it, thank you very much for your help. Sincerely, Dong 在 2019年5月28日星期二 UTC+8下午5:35:
5/28/19
Ales Bucek
,
Minh Bui
2
5/22/19
Q&A
Error when model testing with amino-acid exchange rate matrix and protein mixture models
Hi Ales, The problem is that -mset option is supposed to only specify base substitution models, eg: -
unread,
Answered
Q&A
Error when model testing with amino-acid exchange rate matrix and protein mixture models
Hi Ales, The problem is that -mset option is supposed to only specify base substitution models, eg: -
5/22/19
Max_IT
,
Minh Bui
4
6/3/19
Q&A
bootstrap analysis did not converge. You should rerun with higher number of iterations (-nm option)
Hi Max, I just found the issue, that with -bnni option, this warning is not correct. So please ignore
unread,
Answered
Q&A
bootstrap analysis did not converge. You should rerun with higher number of iterations (-nm option)
Hi Max, I just found the issue, that with -bnni option, this warning is not correct. So please ignore
6/3/19
Marco Forgia
,
Minh Bui
2
5/15/19
Q&A
incomplete sequencences
Hi Marco, On 14 May 2019, at 4:23 pm, Marco Forgia <marco....@unito.it> wrote: Good morning
unread,
Answered
quartetmapping
Q&A
incomplete sequencences
Hi Marco, On 14 May 2019, at 4:23 pm, Marco Forgia <marco....@unito.it> wrote: Good morning
5/15/19
Caio Gueratto Coelho da Silva
,
Minh Bui
2
5/11/19
Q&A
ERROR: File not found JTTDCMut
Hi Caio, Because your alignment contains DNA sequences. The Nexus file says: FORMAT DATATYPE=DNA
unread,
Answered
Q&A
ERROR: File not found JTTDCMut
Hi Caio, Because your alignment contains DNA sequences. The Nexus file says: FORMAT DATATYPE=DNA
5/11/19