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Does -g constraint apply to bootstrap replicates when used with -B, potentially inflating bootstrap support values?

Status: Open.

#152 In iqtree/iqtree3;

· maruiqi0710 opened on Apr 28, 2026

[Feature Request] Feasibility of implementing standard non-parametric bootstrap for CMAPLE / MAPLE

Status: Open.

#150 In iqtree/iqtree3;

· Janzulene opened on Apr 24, 2026

LG_matrice wrong?

Status: Open.

#148 In iqtree/iqtree3;

· MAdriaansens opened on Apr 22, 2026

IQ2MC CRASH WHEN USING PARTITION MODEL

Status: Open.

#145 In iqtree/iqtree3;

· priyanshusingh1301 opened on Apr 7, 2026

SIGABRT crash in ModelFinder when testing duplicate/nested models with +ASC (v3.0.1)

Status: Open.

#143 In iqtree/iqtree3;

· peregrine-t opened on Mar 19, 2026

PMSF might not work correctly in the presence of identical seqs and a potential solution to it

Status: Open.

#139 In iqtree/iqtree3;

· evolbeginner opened on Mar 9, 2026

iqtree3 crash: phylotree.cpp:489: virtual void PhyloTree::setRootNode

Status: Open.

#135 In iqtree/iqtree3;

· hildebra opened on Feb 21, 2026

Add 3di as a data type

enhancementNew feature or requestNew feature or request

modelfinder2

Status: Open.

#134 In iqtree/iqtree3;

· roblanf opened on Feb 17, 2026

modelfinder 2 documentation

Status: Open.

#132 In iqtree/iqtree3;

· roblanf opened on Feb 6, 2026

Disallow LG4M+F and LG4X+F

modelfinder2

Status: Open.

#131 In iqtree/iqtree3;

· thomaskf opened on Feb 6, 2026

add mixture models for modelfinder2

modelfinder2

Status: Open.

#130 In iqtree/iqtree3;

· roblanf opened on Feb 6, 2026

BUG: LSD Phylogenetic Dating does not output any result

Status: Open.

#128 In iqtree/iqtree3;

· Gipsy-The-Sheller opened on Feb 1, 2026