Issues

• Suggestion: adaptive perturbation size

  iqtree/iqtree3#224 · Filter by author roblanf opened on Sep 25, 2026
  1

• Precompiled binary freezes on Arch Linux

  iqtree/iqtree3#221 · Filter by author nrizzo opened on Sep 18, 2026

• -madd models are also fitted in the partition-merging phase, so --merge-model cannot keep merging cheap when a user matrix must be in the final selection

  modelfinder2
  iqtree/iqtree3#219 · Filter by author roblanf opened on Sep 17, 2026

• Confusing user output for Partitionfinder-mAIC

  iqtree/iqtree3#218 · Filter by author roblanf opened on Sep 17, 2026
  1

• Resume from checkpoint failed with "Assertion `i == maxnum-1' failed."

  iqtree/iqtree3#216 · Filter by author SethMusker opened on Sep 10, 2026

• Faster free rates

  modelfinder2
  iqtree/iqtree3#206 · Filter by author roblanf opened on Aug 26, 2026

• Faster -mwopt

  iqtree/iqtree3#205 · Filter by author roblanf opened on Aug 26, 2026

• Logfile and stdout

  iqtree/iqtree3#200 · Filter by author benjamin-lieser opened on Aug 5, 2026

• QC.Mammal frequencies

  iqtree/iqtree3#199 · Filter by author roblanf opened on Aug 5, 2026
  6

• SH-aLRT changes when using jackknife

  iqtree/iqtree3#198 · Filter by author digitalwright opened on Aug 4, 2026
  1

• Jackknife proportion is inverted

  iqtree/iqtree3#196 · Filter by author digitalwright opened on Aug 1, 2026
  1

• Just skip bootstrap if less than 4 sequences instead of error

  iqtree/iqtree3#195 · Filter by author bernt-matthias opened on Aug 1, 2026
  2

• Runtime error: libarcher.so: cannot open shared object file: No such file or directory

  iqtree/iqtree3#189 · Filter by author StefanFlaumberg opened on Jul 19, 2026
  5

• Unclear how to add fossil and secondary calibration dates for MCMCTree

  iqtree/iqtree3#183 · Filter by author ekmcmurchie opened on Jul 7, 2026
  10

• Implement Subtree pruning and regrafting (SPR)

  enhancement
  Feature

  iqtree/iqtree3#181 · Filter by author bqminh opened on Jul 1, 2026
  4

• ModelFinder in IQ-TREE3 could not find the best-fit model

  iqtree/iqtree3#179 · Filter by author jeremiasivan opened on Jun 25, 2026
  3

• GHOST : WARNING: Numerical underflow for lh-derivative-mixlen

  iqtree/iqtree3#171 · Filter by author roisin-long opened on Jun 3, 2026
  7

• tree topology test: docs don't match help options?

  iqtree/iqtree3#166 · Filter by author xvazquezc opened on May 13, 2026
  1

• Segmentation fault when generating Hessian for MCMCTree with large partitioned protein alignment

  iqtree/iqtree3#161 · Filter by author guosongjia opened on May 9, 2026
  4

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

  iqtree/iqtree3#150 · Filter by author Janzulene opened on Apr 24, 2026
  2

• IQ2MC CRASH WHEN USING PARTITION MODEL

  iqtree/iqtree3#145 · Filter by author priyanshusingh1301 opened on Apr 7, 2026
  2

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

  iqtree/iqtree3#143 · Filter by author peregrine-t opened on Mar 19, 2026
  12

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

  iqtree/iqtree3#135 · Filter by author hildebra opened on Feb 21, 2026
  1

• Add 3di as a data type

  enhancementmodelfinder2
  iqtree/iqtree3#134 · Filter by author roblanf opened on Feb 17, 2026
  2

• modelfinder 2 documentation

  iqtree/iqtree3#132 · Filter by author roblanf opened on Feb 6, 2026
  6