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IQ-TREE
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We've now moved to
https://github.com/iqtree/
iqtree2/discussions
. Please ask your question there. This Google group is now closed and for archival purpose only.
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Thomas Wong
1 May
Re: [iqtree] Constrained tree search: problems with version 1.6.12 and 2.3.2
Hi Bastian, Thanks for your message. Can you please try the version 2.3.4 at https://github.com/
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Re: [iqtree] Constrained tree search: problems with version 1.6.12 and 2.3.2
Hi Bastian, Thanks for your message. Can you please try the version 2.3.4 at https://github.com/
1 May
Hung Luong Quoc
,
Bui Quang Minh
2
1 May
How to calculate the distance estimation for amino acid
Please ask this question in github discussions https://github.com/iqtree/iqtree2/discussions. We are
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How to calculate the distance estimation for amino acid
Please ask this question in github discussions https://github.com/iqtree/iqtree2/discussions. We are
1 May
Steve G
,
Bui Quang Minh
2
23 Apr
ERROR: Tree file does not start with an opening-bracket '(' (line 1 column 1)
We're now moving to Github discussions. We'll close down Google group in the near future; it
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ERROR: Tree file does not start with an opening-bracket '(' (line 1 column 1)
We're now moving to Github discussions. We'll close down Google group in the near future; it
23 Apr
Veronica Mantovani Bueno
,
Bui Quang Minh
2
23 Apr
Help with model selection, protein mixture models
Hi Veronia, We're now moving to Github discussions. We'll close down Google group in the near
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Help with model selection, protein mixture models
Hi Veronia, We're now moving to Github discussions. We'll close down Google group in the near
23 Apr
David Cowan
2
22 Apr
Using AliSim to generate synthetic sequences that are similar to input
Just following up on my question. Let me know if its not clear what I am trying to do. Essentially if
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Using AliSim to generate synthetic sequences that are similar to input
Just following up on my question. Let me know if its not clear what I am trying to do. Essentially if
22 Apr
Steve G
,
Bui Quang Minh
2
20 Apr
Getting gCF and sCF values
Are there any error/warning message(s) from the log file. If yes, can you paste them here? (I tend to
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Getting gCF and sCF values
Are there any error/warning message(s) from the log file. If yes, can you paste them here? (I tend to
20 Apr
Akshay Ravoor
,
Bui Quang Minh
3
18 Apr
Issue using IQ-Tree for branch length estimation
Hi Minh, Understood, thank you very much! -- Sincerely, Akshay On Thursday, April 18, 2024 at 12:09:
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Issue using IQ-Tree for branch length estimation
Hi Minh, Understood, thank you very much! -- Sincerely, Akshay On Thursday, April 18, 2024 at 12:09:
18 Apr
Anastasiia
18 Apr
Manage Output Items
Hello All, There used to be options to turn off specific files, for example --no-uniqueseq. Currently
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Manage Output Items
Hello All, There used to be options to turn off specific files, for example --no-uniqueseq. Currently
18 Apr
Bertie
,
Heiko Schmidt
3
17 Apr
CIBIV webserver down?
Hi Heiko, I have discovered that my university wifi/VPN was blocking the CIBIV server (http://iqtree.
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CIBIV webserver down?
Hi Heiko, I have discovered that my university wifi/VPN was blocking the CIBIV server (http://iqtree.
17 Apr
Benjamin Anderson
,
rob.l...@gmail.com
5
16 Apr
Site concordance factors don't sum to 100
Hi Rob, Thanks for digging into this for me! I really appreciate it. My original intention was to
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Site concordance factors don't sum to 100
Hi Rob, Thanks for digging into this for me! I really appreciate it. My original intention was to
16 Apr
Giuseppe Emanuele De Pasquale
, …
Bui Quang Minh
7
15 Apr
Low quality phylogeny
Thanks, Minh! I've identified around 50 rogue taxa using RogueNaRok, and I'm now planning to
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Low quality phylogeny
Thanks, Minh! I've identified around 50 rogue taxa using RogueNaRok, and I'm now planning to
15 Apr
xiaomin liu
, …
Bui Quang Minh
4
14 Apr
ERROR: File not found GTR
Hi Lin, The issue is that IQ-TREE tries to guess the type of sequences by counting the fraction of A,
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ERROR: File not found GTR
Hi Lin, The issue is that IQ-TREE tries to guess the type of sequences by counting the fraction of A,
14 Apr
IQ-TREE
,
Bui Quang Minh
2
14 Apr
a set of tree
Hi Nich, IQ-TREE does maximum likelihood, which produces a single (point estimate) of the tree. But
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a set of tree
Hi Nich, IQ-TREE does maximum likelihood, which produces a single (point estimate) of the tree. But
14 Apr
Simone Gable
,
Bui Quang Minh
2
14 Apr
Redo Tree Inference Only
You can use this option: --redo-tree Restore ModelFinder and only redo tree search Cheers, Minh On
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Redo Tree Inference Only
You can use this option: --redo-tree Restore ModelFinder and only redo tree search Cheers, Minh On
14 Apr
gree...@gmail.com
,
Sishuo Wang
5
12 Apr
AliSim with site-specific frequency profiles
Dear Mattia, You are right at poinitng out that the word "iterative" used in my 1st reply
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AliSim with site-specific frequency profiles
Dear Mattia, You are right at poinitng out that the word "iterative" used in my 1st reply
12 Apr
IQ-TREE
,
Bui Quang Minh
2
10 Apr
invalid option
Hi Nich, Please send the command line here, it's hard to know without seeing it. Cheers, Minh On
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invalid option
Hi Nich, Please send the command line here, it's hard to know without seeing it. Cheers, Minh On
10 Apr
CR Cardenas
,
Bui Quang Minh
4
10 Apr
gene tree output, what is the order of the treefile?
Hi Cardenas, The gene trees in treefile should be in the same order as the input partition file,
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gene tree output, what is the order of the treefile?
Hi Cardenas, The gene trees in treefile should be in the same order as the input partition file,
10 Apr
Helga Cassol
10 Apr
Process killed during model finding
Dear all, I'm trying to build a tree from some alignment files in phy format. These files come
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Process killed during model finding
Dear all, I'm trying to build a tree from some alignment files in phy format. These files come
10 Apr
Alexandra Gavryushkina
8 Apr
Dating existing trees with ages not matching the original ones
Hi developers, Could you please help us with dating trees. We have a tree in a newick format,
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Dating existing trees with ages not matching the original ones
Hi developers, Could you please help us with dating trees. We have a tree in a newick format,
8 Apr
Matias Wanntorp
6 Apr
iq-tree getting stuck using PMSF approximation and -bnni
Hello, I have been trying to run iqtree with LG+C60+G+F with PMSF -bb 1000 -bnni however it gets
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iq-tree getting stuck using PMSF approximation and -bnni
Hello, I have been trying to run iqtree with LG+C60+G+F with PMSF -bb 1000 -bnni however it gets
6 Apr
Sara Rocha
,
Heiko Schmidt
2
2 Apr
run "killed" at start - reasons?
Dear Sara, Thank you for your interest in IQ-TREE. From the output you have shown and my knowledge
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run "killed" at start - reasons?
Dear Sara, Thank you for your interest in IQ-TREE. From the output you have shown and my knowledge
2 Apr
ear...@gmail.com
31 Mar
Custom *set* of initial trees from file
Hello everyone, I would like to do a tree search providing my own set of initial trees, but it looks
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Custom *set* of initial trees from file
Hello everyone, I would like to do a tree search providing my own set of initial trees, but it looks
31 Mar
Daniela Araya
21 Mar
st Codon error IQTree2
Hello, I getting this error when I'm trying to run -st CODON and I'm not sure what I need to
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st Codon error IQTree2
Hello, I getting this error when I'm trying to run -st CODON and I'm not sure what I need to
21 Mar
Reiss Jordynn
15 Mar
ERROR - Sorry, there is an issue with the cluster system. We are trying to resolve it asap!
Hi, I am trying to submit a fa file into iq tree, and it used to work before but give me the error
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ERROR - Sorry, there is an issue with the cluster system. We are trying to resolve it asap!
Hi, I am trying to submit a fa file into iq tree, and it used to work before but give me the error
15 Mar
임원섭 / 학생 / 지구과학교육과
9 Mar
-wsl printing results of the last run, not the best run when using --runs option
Hi, I was conducting some analysis involving site-wise log-likelihood calculation, and found that
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-wsl printing results of the last run, not the best run when using --runs option
Hi, I was conducting some analysis involving site-wise log-likelihood calculation, and found that
9 Mar
jc
7 Mar
Bug or intended behavior? -v suppresses branch support
Hi IQ-Tree team, I ran into some unexpected behavior from IQ-Tree recently that I wanted to document
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Bug or intended behavior? -v suppresses branch support
Hi IQ-Tree team, I ran into some unexpected behavior from IQ-Tree recently that I wanted to document
7 Mar
Robert Jones
5 Mar
Help running a partitioned analysis with mixed data types
Hi all, I have been trying to run a partitioned analysis with mixed data types in IQ-TREE2. It has
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Help running a partitioned analysis with mixed data types
Hi all, I have been trying to run a partitioned analysis with mixed data types in IQ-TREE2. It has
5 Mar
陳鴻文(Hong-Wun Chen)
2
5 Mar
How to write ultrafast bootstrap trees with branch lengths?
Here is some detail of my version , etc IQ-TREE multicore version 2.2.6 COVID-edition for Linux 64-
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How to write ultrafast bootstrap trees with branch lengths?
Here is some detail of my version , etc IQ-TREE multicore version 2.2.6 COVID-edition for Linux 64-
5 Mar
Alexander Nagy
,
Hien To
2
5 Mar
Help with dating a phylogenetic tree
Hi Alexander, If it's possible, could you send me the data so I can inspect? Cheers, Hien On Mon,
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Help with dating a phylogenetic tree
Hi Alexander, If it's possible, could you send me the data so I can inspect? Cheers, Hien On Mon,
5 Mar
Zachary Griebenow
4 Mar
Partition log-likelihoods for alternative topologies, v. 2.1.2
Greetings all, I would like to calculate partition log-likelihood scores for two alternative
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Partition log-likelihoods for alternative topologies, v. 2.1.2
Greetings all, I would like to calculate partition log-likelihood scores for two alternative
4 Mar