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IQ-TREE
1–28 of 1859
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iqtree2/discussions
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Will Hamilton
,
Minh Bui
6
7/14/20
Q&A
Quantify support for branch nodes in tree reconstruction
Oh, This is because you didn't perform bootstrap, that's something I missed from your first
unread,
Bootstrap
Question
branch
iqtree
node
tree
Q&A
Quantify support for branch nodes in tree reconstruction
Oh, This is because you didn't perform bootstrap, that's something I missed from your first
7/14/20
Gabriel DUPRE
,
Minh Bui
2
6/12/20
Q&A
What are the differences between the user-provided tree file and the ".treefile", generated from an ASR job?
Hi Gabriel, On 12 Jun 2020, at 6:42 pm, Gabriel DUPRE <gabriel...@gmail.com> wrote: Hi, I
unread,
ASR
Question
Q&A
What are the differences between the user-provided tree file and the ".treefile", generated from an ASR job?
Hi Gabriel, On 12 Jun 2020, at 6:42 pm, Gabriel DUPRE <gabriel...@gmail.com> wrote: Hi, I
6/12/20
Kuselah Tayaban
, …
Minh Bui
7
6/9/20
Q&A
data input error
Hi Minh, I forgot to check file permission. It already worked! Thanks a lot, Kuselah On Tuesday, June
unread,
IQtreeErrors
Question
error
iqtree
Q&A
data input error
Hi Minh, I forgot to check file permission. It already worked! Thanks a lot, Kuselah On Tuesday, June
6/9/20
Tricia Goulding
,
Minh Bui
3
6/19/20
Q&A
Phylogenetic dating - calibration and confidence intervals
Hi Minh and Hien, Thank you for your responses to my issue. I have downloaded v.2.0.6 and this fixed
unread,
Question
Q&A
Phylogenetic dating - calibration and confidence intervals
Hi Minh and Hien, Thank you for your responses to my issue. I have downloaded v.2.0.6 and this fixed
6/19/20
DR
,
Minh Bui
2
5/7/20
Q&A
Question about performance of partition models
Hi there, Can you please provide more context about your data, eg, how many partitions, sequences,
unread,
MODEL
Partition
Question
Q&A
Question about performance of partition models
Hi there, Can you please provide more context about your data, eg, how many partitions, sequences,
5/7/20
Sarah Lock
,
Minh Bui
2
4/27/20
Q&A
IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT? - version 1.6.6
Hi Sarah, There is something wrong in the PLL library used internally in IQ-TREE to compute a
unread,
BUG
IQtreeErrors
Partition
Question
Request
error
iqtree
Q&A
IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT? - version 1.6.6
Hi Sarah, There is something wrong in the PLL library used internally in IQ-TREE to compute a
4/27/20
John Soghigian
,
Minh Bui
2
11/10/19
Q&A
what happens to sites not specified in a partition file?
Hi John, The simple answer is Yes, IQ-TREE will ignore all positions not included in the partition
unread,
Partition
Question
codon
Q&A
what happens to sites not specified in a partition file?
Hi John, The simple answer is Yes, IQ-TREE will ignore all positions not included in the partition
11/10/19
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
John jiang
,
Minh Bui
2
6/26/19
Q&A
For your convenience alignment with variable sites printed to file.phy
Hi John, Please first have a look at this FAQ: http://www.iqtree.org/doc/Frequently-Asked-Questions#
unread,
IQtreeErrors
Question
SNP
Q&A
For your convenience alignment with variable sites printed to file.phy
Hi John, Please first have a look at this FAQ: http://www.iqtree.org/doc/Frequently-Asked-Questions#
6/26/19
Jacopo Martelossi
,
Minh Bui
5
6/12/19
Q&A
constrained tree search approach
Hi Jacopo, This problem was discussed and answered here: https://groups.google.com/forum/#!topic/
unread,
Question
test
tree
Q&A
constrained tree search approach
Hi Jacopo, This problem was discussed and answered here: https://groups.google.com/forum/#!topic/
6/12/19
Chang Ye
,
Minh Bui
8
5/29/19
Q&A
How to select model for binary irreversible sequence data?
Hi Minh Thanks for your advice. On Tue, May 28, 2019 at 9:06 AM Minh Bui <minh...@univie.ac.at
unread,
Answered
MODEL
Question
irreversible
rate
Q&A
How to select model for binary irreversible sequence data?
Hi Minh Thanks for your advice. On Tue, May 28, 2019 at 9:06 AM Minh Bui <minh...@univie.ac.at
5/29/19
Edward Braun
, …
Minh Bui
6
9/22/20
Q&A
Model selection for Lie Markov models
You don't need to provide a tree, IQ-TREE will find the root automatically. Minh On 14 Sep 2020,
unread,
Answered
MODEL
Question
Q&A
Model selection for Lie Markov models
You don't need to provide a tree, IQ-TREE will find the root automatically. Minh On 14 Sep 2020,
9/22/20
Alejandro Edera
, …
Bui Quang Minh
4
1/28/18
Q&A
Interpreting the matrix Q
Hi, On Saturday, 27 January 2018 09:22:15 UTC-3, Bui Quang Minh wrote: Hi there, Firstly please
unread,
Answered
Question
calculation
rate
Q&A
Interpreting the matrix Q
Hi, On Saturday, 27 January 2018 09:22:15 UTC-3, Bui Quang Minh wrote: Hi there, Firstly please
1/28/18
Will Chase
,
Bui Quang Minh
6
1/4/18
Q&A
Hetertachy models in modelfinder
Hi Will, This is a typically difficult data set due to short sequences. Reducing number of sequences
unread,
Answered
Question
heterotachy
Q&A
Hetertachy models in modelfinder
Hi Will, This is a typically difficult data set due to short sequences. Reducing number of sequences
1/4/18
Lucas Marques
,
Bui Quang Minh
3
11/24/17
Q&A
IQ-tree's method for least-squares AU implementation
Thanks for your quick reply, Minh. This will be very helpful. I'll take a close look at the code
unread,
Answered
Question
calculation
Q&A
IQ-tree's method for least-squares AU implementation
Thanks for your quick reply, Minh. This will be very helpful. I'll take a close look at the code
11/24/17
Bui Quang Minh
11/20/17
Re: IQ-TREE “-m C60+LG+G+F” vs “-m LG+C60+G+F”
Hi Ding, This is a very good remark, thus I'm replying to the IQ-TREE forum here, in case other
unread,
Question
Re: IQ-TREE “-m C60+LG+G+F” vs “-m LG+C60+G+F”
Hi Ding, This is a very good remark, thus I'm replying to the IQ-TREE forum here, in case other
11/20/17
Kristian Davidsen
, …
Bui Quang Minh
4
2/8/18
Q&A
Just maximum parsimony tree?
Dear Tamara, Your question came just in time ;-) We recently published a paper on this: DT Hoang, LS
unread,
Answered
Question
Q&A
Just maximum parsimony tree?
Dear Tamara, Your question came just in time ;-) We recently published a paper on this: DT Hoang, LS
2/8/18
Anthony Redmond
,
Bui Quang Minh
5
12/12/17
Q&A
Implementation of combined mixture models (e.g. JTT+UL3+G)
Dear Minh, Sounds great! Thanks again, Anthony On Tuesday, December 12, 2017 at 3:21:09 PM UTC, Bui
unread,
Question
Resolved
Q&A
Implementation of combined mixture models (e.g. JTT+UL3+G)
Dear Minh, Sounds great! Thanks again, Anthony On Tuesday, December 12, 2017 at 3:21:09 PM UTC, Bui
12/12/17
Joran Martijn
, …
Robyn Lee
13
8/8/18
Q&A
A bootstrap tree with a higher likelihood for the original alignment than the ML tree for that alignment
Hi Minh, Ok, thank you very much for letting me know and sharing for the details. Have a nice day.
unread,
Question
Resolved
Q&A
A bootstrap tree with a higher likelihood for the original alignment than the ML tree for that alignment
Hi Minh, Ok, thank you very much for letting me know and sharing for the details. Have a nice day.
8/8/18
kin onn chan
,
Bui Quang Minh
2
11/4/17
Q&A
Model selection on large genomic dataset
Hi Chan, While I don't know your expectation about what is satisfactory or not, my recommendation
unread,
Question
Q&A
Model selection on large genomic dataset
Hi Chan, While I don't know your expectation about what is satisfactory or not, my recommendation
11/4/17
Arshia shafagh
, …
Bui Quang Minh
3
10/30/17
Q&A
partitioning by genes and codons
Thanks Siby! I just want to add the link: http://www.iqtree.org/doc/Complex-Models#partition-models.
unread,
Question
Q&A
partitioning by genes and codons
Thanks Siby! I just want to add the link: http://www.iqtree.org/doc/Complex-Models#partition-models.
10/30/17
Alfredo Rodríguez Arteaga
,
Bui Quang Minh
3
10/15/17
Q&A
Can you rebuild a tree from where it stopped? The construction of my tree was stopped because of a problem in my machine.
Hi Alfredo, That's right, good that you found the solution yourself ;-) Moreover, another tip:
unread,
Question
Q&A
Can you rebuild a tree from where it stopped? The construction of my tree was stopped because of a problem in my machine.
Hi Alfredo, That's right, good that you found the solution yourself ;-) Moreover, another tip:
10/15/17
JChan
,
Stephen Crotty
4
10/4/17
Q&A
how to use "testnew" commend?
Hi Joanna, This error occurs to make sure that you don't accidentally overwrite the output from a
unread,
Question
Q&A
how to use "testnew" commend?
Hi Joanna, This error occurs to make sure that you don't accidentally overwrite the output from a
10/4/17
Alexandros Vasilikopoulos
,
Bui Quang Minh
4
10/5/17
Q&A
MERGE PARTITIONS WEIGHTS-CRITERIA
Hi Alex, With rates I mean the sum of branch lengths of the partition tree (or tree length). Fast/
unread,
Question
Q&A
MERGE PARTITIONS WEIGHTS-CRITERIA
Hi Alex, With rates I mean the sum of branch lengths of the partition tree (or tree length). Fast/
10/5/17
Gavin Martin
,
Heiko Schmidt
5
9/15/17
Q&A
Problem with constrain File
Thank you, it looks like the problem was that I had single entities within their own brackets. All
unread,
IQtreeErrors
Question
Q&A
Problem with constrain File
Thank you, it looks like the problem was that I had single entities within their own brackets. All
9/15/17
Xabier Vázquez-Campos
, …
taua...@gmail.com
8
9/26/17
Q&A
usage of PMSF
Hi again Stephen, I was missing a connection from my definition to how the problem is actually
unread,
Answered
BEST
MODEL
PMSF
Question
Q&A
usage of PMSF
Hi again Stephen, I was missing a connection from my definition to how the problem is actually
9/26/17
Joaquim Martins Junior
,
Bui Quang Minh
4
2/16/16
Q&A
IQTree 1.3.13 crashes during tree search with partitioned dataset
Dear Joachim, as it turned out the crash was likely due to -vvv option (verbose mode). This option
unread,
BUG
Question
Q&A
IQTree 1.3.13 crashes during tree search with partitioned dataset
Dear Joachim, as it turned out the crash was likely due to -vvv option (verbose mode). This option
2/16/16
joanpo...@gmail.com
,
Bui Quang Minh
3
12/2/15
Q&A
ERROR: Invalid model name GTR
Hi Joan, please recode the 3rd codon sites into 0 and 1 (instead of R and Y). Then iqtree
unread,
Question
Q&A
ERROR: Invalid model name GTR
Hi Joan, please recode the 3rd codon sites into 0 and 1 (instead of R and Y). Then iqtree
12/2/15