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IQ-TREE
1–30 of 1859
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iqtree2/discussions
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Christian Rinke
,
Minh Bui
6
7/9/19
Q&A
Bootstrap <1%issue
Alright, I could reproduce this now. My next question is: how did you reconstruct this tree? When I
unread,
Resolved
Q&A
Bootstrap <1%issue
Alright, I could reproduce this now. My next question is: how did you reconstruct this tree? When I
7/9/19
Minh Bui
2
7/3/19
Fwd: Iqtree bug report
Dear Yang Song, Thanks for the report. To help us reproduce this behaviour, please send us all the
unread,
Resolved
Fwd: Iqtree bug report
Dear Yang Song, Thanks for the report. To help us reproduce this behaviour, please send us all the
7/3/19
Sishuo Wang
,
Minh Bui
7
7/3/19
Q&A
Pairwise distance in .mldist
Hi Sishuo, I had a thorough look and it looks like there is a bug in distance computation (.mldist
unread,
Resolved
Q&A
Pairwise distance in .mldist
Hi Sishuo, I had a thorough look and it looks like there is a bug in distance computation (.mldist
7/3/19
Teofil Nakov
,
Minh Bui
2
5/30/19
Q&A
Partitioning by codon syntax
Hi Teo, This syntax is not supported in IQ-TREE (actually I was not aware of it). But it's a
unread,
Resolved
Q&A
Partitioning by codon syntax
Hi Teo, This syntax is not supported in IQ-TREE (actually I was not aware of it). But it's a
5/30/19
Emmanuel Cantú
,
Minh Bui
2
3/17/19
Q&A
Bug report- IQ-TREE CRASHES WITH SIGNAL ABORTED
Hi Emmanuel, CC Diep, It looks like -bnni option does not work with GENE resampling (-bspec GENE)… We
unread,
Resolved
Q&A
Bug report- IQ-TREE CRASHES WITH SIGNAL ABORTED
Hi Emmanuel, CC Diep, It looks like -bnni option does not work with GENE resampling (-bspec GENE)… We
3/17/19
Bradley Martin
,
Minh Bui
4
2/5/19
Q&A
BUG: iqtree 1.7-beta7 Concordance Factors - Assertion `!aln->ordered_pattern.empty()' failed
Hello, Thank you for your insight and prompt reply. I will probably filter out the non-informative
unread,
Resolved
Q&A
BUG: iqtree 1.7-beta7 Concordance Factors - Assertion `!aln->ordered_pattern.empty()' failed
Hello, Thank you for your insight and prompt reply. I will probably filter out the non-informative
2/5/19
Sarah Mathews
,
Sarah....@csiro.au
3
1/16/19
Q&A
ERROR: Tree file does not start with an opening-bracket
Hi Minh, Thanks, I do remember reading that. I'll set number of cores. Cheers Sarah Sent from my
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Resolved
Q&A
ERROR: Tree file does not start with an opening-bracket
Hi Minh, Thanks, I do remember reading that. I'll set number of cores. Cheers Sarah Sent from my
1/16/19
Mark Miller
,
Minh Bui
3
2/19/19
Q&A
ERROR: Tree file does not start with an opening-bracket
Dear Mark, This issue is now fixed in version 1.6.10 just released. Thanks, Minh On 17 Jan 2019, at 5
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Resolved
Q&A
ERROR: Tree file does not start with an opening-bracket
Dear Mark, This issue is now fixed in version 1.6.10 just released. Thanks, Minh On 17 Jan 2019, at 5
2/19/19
Manuela Cascini
,
Minh Bui
2
1/8/19
Q&A
Crashes with signal erroneous numeric
Dear Manu, Can you please use the latest version 1.6.9 and let me know if it works or not? If not,
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Resolved
Q&A
Crashes with signal erroneous numeric
Dear Manu, Can you please use the latest version 1.6.9 and let me know if it works or not? If not,
1/8/19
Aaron Liston
, …
nicola...@gmail.com
5
12/17/18
Q&A
BUG: concordance factors
Hi Minh, Thank you very much for your message. I have downloaded the last version. The new version
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Resolved
Q&A
BUG: concordance factors
Hi Minh, Thank you very much for your message. I have downloaded the last version. The new version
12/17/18
Cecile Ane
,
Minh Bui
3
12/3/18
Q&A
identical sequences not added at the end with the --no-outfiles option
Thank you Minh!
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Resolved
Q&A
identical sequences not added at the end with the --no-outfiles option
Thank you Minh!
12/3/18
Nathanael Walker-Hale
,
Minh Bui
7
12/19/18
Q&A
-asr with codons
Yes, in general when you have enough data it should work. Minh On 20 Dec 2018, at 9:36 am, Nathanael
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Resolved
Q&A
-asr with codons
Yes, in general when you have enough data it should work. Minh On 20 Dec 2018, at 9:36 am, Nathanael
12/19/18
Michael Raupach
,
Minh Bui
2
11/29/18
Q&A
Wrong reference in the manual?
Hi Michael, You are right! This ref is for the mtREV model. Thanks for pointing it out. We will fix
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Resolved
Q&A
Wrong reference in the manual?
Hi Michael, You are right! This ref is for the mtREV model. Thanks for pointing it out. We will fix
11/29/18
Trevor Bedford
,
Minh Bui
4
12/16/18
Q&A
BUG: SIGNAL SEGMENTATION FAULT in v1.6.8
Hi Trevor, I've tested this run on my Mac and Linux and nothing crashed at all. However, I also
unread,
Resolved
homebrew_issue
Q&A
BUG: SIGNAL SEGMENTATION FAULT in v1.6.8
Hi Trevor, I've tested this run on my Mac and Linux and nothing crashed at all. However, I also
12/16/18
ppu...@humboldt.org.co
,
Minh Bui
3
11/15/18
Q&A
IQ-TREE version 1.6.5 - crash segmentation fault
Thanks. It worked :) El miércoles, 14 de noviembre de 2018, 21:38:21 (UTC-5), Minh Bui escribió: Hi
unread,
Resolved
Q&A
IQ-TREE version 1.6.5 - crash segmentation fault
Thanks. It worked :) El miércoles, 14 de noviembre de 2018, 21:38:21 (UTC-5), Minh Bui escribió: Hi
11/15/18
Morgan Jackson
,
Minh Bui
2
11/6/18
Q&A
"ERROR: Cannot concatenate sub-alignments of different #states"
Hi Morgan, Many thanks for the report. I confirm this is a problem in IQ-Tree. I overlooked that a
unread,
Resolved
Q&A
"ERROR: Cannot concatenate sub-alignments of different #states"
Hi Morgan, Many thanks for the report. I confirm this is a problem in IQ-Tree. I overlooked that a
11/6/18
Denis Jacob Machado
,
Minh Bui
3
11/4/18
Q&A
Why is IQ-Tree ignoring terminals with only morphological data in my total evidence analysis?
Dear Dr. Minh Bui, Thank you for the explanation, I was having difficulties finding this error by
unread,
Resolved
lost-terminal
missing
morphology
total-evicence
tree
Q&A
Why is IQ-Tree ignoring terminals with only morphological data in my total evidence analysis?
Dear Dr. Minh Bui, Thank you for the explanation, I was having difficulties finding this error by
11/4/18
Michele Leocádio
,
Minh Bui
2
10/22/18
Q&A
BUG (?): IQTREE crashing when running MF
Hi Michele, Can you please send here the screenshot of the crash message/window? Thanks Minh On 22
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ModelFinder
Resolved
Q&A
BUG (?): IQTREE crashing when running MF
Hi Michele, Can you please send here the screenshot of the crash message/window? Thanks Minh On 22
10/22/18
Paul Frandsen
, …
Minh Bui
9
3/31/19
Q&A
BUG? mixed binary/nucleotide analysis
Hi Cristina, Did you try the latest version (1.6.10)? I believe this problem was fixed… Minh On 30
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Resolved
Q&A
BUG? mixed binary/nucleotide analysis
Hi Cristina, Did you try the latest version (1.6.10)? I believe this problem was fixed… Minh On 30
3/31/19
Fritjof La
,
Minh Bui
4
10/27/18
Q&A
Dollo-like substituion model for binary characters
Hi Fritjof, Sorry for the slow response. I looked at such model and there is numerical issue with the
unread,
Resolved
v168
Q&A
Dollo-like substituion model for binary characters
Hi Fritjof, Sorry for the slow response. I looked at such model and there is numerical issue with the
10/27/18
Dan Proud
, …
Minh Bui
8
1/31/19
Q&A
Approximately Unbiased test returns p-value of 1.0 while other tests are significant
Hi Karen again, Yes this problem with v1.6.8 was fixed in v1.6.9, see the release note: http://www.
unread,
AU_test
Resolved
likelihood
topology
user_trees
Q&A
Approximately Unbiased test returns p-value of 1.0 while other tests are significant
Hi Karen again, Yes this problem with v1.6.8 was fixed in v1.6.9, see the release note: http://www.
1/31/19
Alexey Kozlov
,
Minh Bui
4
7/21/18
Q&A
IQTREE 1.6.6 incorrectly handles RAxML-style partition files with multiple blocks
Hi Alexey, I tried with an example data set here and IQ-TREE v1.6.6 loaded correctly (ie fragmented
unread,
BUG
Resolved
Q&A
IQTREE 1.6.6 incorrectly handles RAxML-style partition files with multiple blocks
Hi Alexey, I tried with an example data set here and IQ-TREE v1.6.6 loaded correctly (ie fragmented
7/21/18
stra...@protist.eu
,
Minh Bui
4
8/5/18
Q&A
Not enough memory
Hi Jürgen, Not yet, but one thing that could help: use "-mem 120G”. This will restrict the RAM
unread,
Resolved
Q&A
Not enough memory
Hi Jürgen, Not yet, but one thing that could help: use "-mem 120G”. This will restrict the RAM
8/5/18
Cloud LI
7/10/18
long branch and unrealible results in the runing
I used the PF2 results into iqtree, and it runs successfully, but I got an unreliable result compared
unread,
Resolved
long branch and unrealible results in the runing
I used the PF2 results into iqtree, and it runs successfully, but I got an unreliable result compared
7/10/18
stra...@protist.eu
,
Minh Bui
7
7/9/18
Q&A
difference LG+C40 and LG+C40+G
Hi Juergen, +F will be considered. Ie your model below is a profile mixture model with 41 classes, 40
unread,
Resolved
Q&A
difference LG+C40 and LG+C40+G
Hi Juergen, +F will be considered. Ie your model below is a profile mixture model with 41 classes, 40
7/9/18
Karen Meusemann
,
Minh Bui
5
6/30/18
Q&A
Bug - pllPartitionsValidate
Hi Minh, all jobs succesfully finished (with the last beta version (1.6.6.c) :) many many thanks for
unread,
Resolved
Q&A
Bug - pllPartitionsValidate
Hi Minh, all jobs succesfully finished (with the last beta version (1.6.6.c) :) many many thanks for
6/30/18
Andrew Swafford
2
6/6/18
Q&A
IQtree 1.6.5 crash - "Assertion `freq_type != FREQ_UNKNOWN' failed"
I noticed this is a possible bug when using LG4M and LG4X in 1.6.5, see thread here: https://groups.
unread,
Resolved
Q&A
IQtree 1.6.5 crash - "Assertion `freq_type != FREQ_UNKNOWN' failed"
I noticed this is a possible bug when using LG4M and LG4X in 1.6.5, see thread here: https://groups.
6/6/18
giddy....@gmail.com
, …
Minh Bui
4
6/6/18
Q&A
BUG: 1.6.5 crash on -madd LG4M and LG4X
Hi Karen and others, This issue is fixed in a local version here (just one line of code). I need to
unread,
Resolved
Q&A
BUG: 1.6.5 crash on -madd LG4M and LG4X
Hi Karen and others, This issue is fixed in a local version here (just one line of code). I need to
6/6/18
jp.fland...@gmail.com
,
Minh Bui
3
5/30/18
Q&A
the / separating the support values are replace by _
Hi Minh I will revert to 1.6.4 because all the wraper is using the / tag to compute a composite
unread,
Resolved
Q&A
the / separating the support values are replace by _
Hi Minh I will revert to 1.6.4 because all the wraper is using the / tag to compute a composite
5/30/18
Giap Nguyen
, …
Minh Bui
4
5/10/18
ERROR: Number of Likelihood Mapping groups too high
Dear Giap, --runs option does not work with -lmap yet, because it's meant for multiple tree
unread,
Resolved
ERROR: Number of Likelihood Mapping groups too high
Dear Giap, --runs option does not work with -lmap yet, because it's meant for multiple tree
5/10/18