Hi Gabriel, I suggest that you avoid doing codon models for tree reconstruction for your dataset:

Dear Alexey, Two additional comments in addition to those of Minh and Rob: > On 28 Jun 2020, at 20

Hi Gabriel, Simple answer: you forgot to set the sequence type as codon: -st CODON (for standard

Dear Adrià, I am not an expert on it. As follows i try to share w you some of my perhaps naive

Hi Bastian, Thanks for your message. Can you please try the version 2.3.4 at https://github.com/

Please ask this question in github discussions https://github.com/iqtree/iqtree2/discussions. We are

We're now moving to Github discussions. We'll close down Google group in the near future; it

Hi Veronia, We're now moving to Github discussions. We'll close down Google group in the near

Just following up on my question. Let me know if its not clear what I am trying to do. Essentially if

Are there any error/warning message(s) from the log file. If yes, can you paste them here? (I tend to

Hi Minh, Understood, thank you very much! -- Sincerely, Akshay On Thursday, April 18, 2024 at 12:09:

Hello All, There used to be options to turn off specific files, for example --no-uniqueseq. Currently

Hi Heiko, I have discovered that my university wifi/VPN was blocking the CIBIV server (http://iqtree.

Hi Rob, Thanks for digging into this for me! I really appreciate it. My original intention was to

Thanks, Minh! I've identified around 50 rogue taxa using RogueNaRok, and I'm now planning to

Hi Lin, The issue is that IQ-TREE tries to guess the type of sequences by counting the fraction of A,

Hi Nich, IQ-TREE does maximum likelihood, which produces a single (point estimate) of the tree. But

You can use this option: --redo-tree Restore ModelFinder and only redo tree search Cheers, Minh On

Dear Mattia, You are right at poinitng out that the word "iterative" used in my 1st reply

Hi Nich, Please send the command line here, it's hard to know without seeing it. Cheers, Minh On

Hi Cardenas, The gene trees in treefile should be in the same order as the input partition file,

Dear all, I'm trying to build a tree from some alignment files in phy format. These files come

Hi developers, Could you please help us with dating trees. We have a tree in a newick format,

Hello, I have been trying to run iqtree with LG+C60+G+F with PMSF -bb 1000 -bnni however it gets

Dear Sara, Thank you for your interest in IQ-TREE. From the output you have shown and my knowledge

Hello everyone, I would like to do a tree search providing my own set of initial trees, but it looks

Hello, I getting this error when I'm trying to run -st CODON and I'm not sure what I need to

Hi, I am trying to submit a fa file into iq tree, and it used to work before but give me the error

Hi, I was conducting some analysis involving site-wise log-likelihood calculation, and found that

Hi IQ-Tree team, I ran into some unexpected behavior from IQ-Tree recently that I wanted to document

Hi all, I have been trying to run a partitioned analysis with mixed data types in IQ-TREE2. It has

Here is some detail of my version , etc IQ-TREE multicore version 2.2.6 COVID-edition for Linux 64-

Hi Alexander, If it's possible, could you send me the data so I can inspect? Cheers, Hien On Mon,