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-te flag does not constrain tree when using --scfl

Status: Open.

#85 In iqtree/iqtree3;

· stiatragul opened on Sep 3, 2025

Question on ModelFinder in IQ-TREE 3: mixture of reversible and non-reversible models

Status: Open.

#84 In iqtree/iqtree3;

· dongzhang0725 opened on Sep 2, 2025

"ERROR: Tree taxa and alignment sequence do not match" when supplying starting tree with -t

Status: Open.

#82 In iqtree/iqtree3;

· SethMusker opened on Aug 20, 2025

[BUG] Unable to disable <code>+ASC</code> in ModelFinder for partitioned models

Status: Open.

#80 In iqtree/iqtree3;

· HS6986 opened on Aug 11, 2025

[BUG] iqtree3 and 2 cannot get a tree for an alignment file.

Status: Open.

#74 In iqtree/iqtree3;

· anand-ll opened on Jun 30, 2025

[BUG] -madd not working in MFP and MF with IQtree3

Status: Open.

#65 In iqtree/iqtree3;

· dorohuchon opened on Jun 21, 2025

Dating with LSD2 not running in iqtree3?

Status: Open.

#63 In iqtree/iqtree3;

· charlesfoster opened on Jun 19, 2025

--robust-phy doesn't work with a partition file

Status: Open.

#60 In iqtree/iqtree3;

· Rohit-Rannavre opened on Jun 12, 2025

PMSF Step 1: '+I' Proportion of Invariable Sites Not Correctly Estimated in IQ-TREE v3.0.1

Status: Open.

#58 In iqtree/iqtree3;

· Yutong-Shao opened on Jun 4, 2025

[BUG] The site-specific frequency model with "+ASC+G4" crashes, but the models with "+ASC" or "+G4" do not

Status: Open.

#55 In iqtree/iqtree3;

· HS6986 opened on May 31, 2025

PMSF crashes on some, but not all, morphological datasets

Status: Open.

#54 In iqtree/iqtree3;

· HS6986 opened on May 29, 2025

PMSF on morphological data crashes with the <code>+ASC</code> flag

Status: Open.

#52 In iqtree/iqtree3;

· HS6986 opened on May 28, 2025