Issues

• iqtree.org TLS certificate expired (4 May 2025); documentation unreachable over HTTPS

  iqtree/iqtree2#542 · Filter by author ssiddhantsharma opened on Sep 6, 2026

• Checkpoint file not updated during --root-test (NONREV) phase in IQ-TREE 3.1.3 MPI

  iqtree/iqtree2#536 · Filter by author BenMcDUON opened on Jul 19, 2026

• -wslr/-wslm .sitelh violates its own sum(exp(LnLW_k)) == exp(LnL) invariant for codon/morphology models

  iqtree/iqtree2#533 · Filter by author famulare opened on Jul 7, 2026

• -m MFP = default?

  modelfinder2
  iqtree/iqtree2#514 · Filter by author roblanf opened on Jan 28, 2026
  1

• Partition merging .best_model format issues

  modelfinder2
  iqtree/iqtree2#513 · Filter by author roblanf opened on Jan 28, 2026

• Iqtree not producing splits.nex file

  iqtree/iqtree2#509 · Filter by author ts-dangelo opened on Dec 22, 2025

• Dear Fabricia,

  iqtree/iqtree2#504 · Filter by author leandrosenadefigueiredo-lgtm opened on Dec 5, 2025

• IQ-TREE CRASHES WITH SIGNAL ABORTED

  iqtree/iqtree2#493 · Filter by author sttongjai opened on Oct 8, 2025
  2

• Likelihood mapping: quartet mapping reduced to unique quartets but iqtree performs more calculations than the number of unique quartets

  iqtree/iqtree2#489 · Filter by author AlesBucek opened on Sep 17, 2025

• Rooted Tree Input for Ancestral Reconstruction

  iqtree/iqtree2#481 · Filter by author dafnago2 opened on Aug 20, 2025
  8

• '-bnni' causes 'core dump' when using '-S' to reconstruct trees in a folder

  iqtree/iqtree2#479 · Filter by author bingli8899 opened on Jul 25, 2025

• Is it possible to estimate profile mixtures under LG or any empirical exchangeability matrix using iqtree?

  iqtree/iqtree2#477 · Filter by author evolbeginner opened on Jul 11, 2025

• unable to load server

  iqtree/iqtree2#474 · Filter by author jmajanja opened on Jun 17, 2025
  1

• Time tree reconstruction - branch distances seem off

  iqtree/iqtree2#471 · Filter by author alanxelena opened on Jun 10, 2025
  14

• ERROR: phylotree.cpp:4072 XXX failed

  iqtree/iqtree2#469 · Filter by author quliping opened on Jun 3, 2025
  1

• ERROR: STACK TRACE FOR DEBUGGING

  iqtree/iqtree2#465 · Filter by author viskky opened on May 15, 2025
  2

• Codon model requirements

  iqtree/iqtree2#464 · Filter by author roblanf opened on May 9, 2025
  1

• IQtree2 build tree for 200 humans with 6,000,000 SNPs

  iqtree/iqtree2#463 · Filter by author BrendaLee1 opened on May 8, 2025
  2

• ModelTamer

  modelfinder2
  iqtree/iqtree2#460 · Filter by author roblanf opened on May 6, 2025
  2

• Segmentation Fault when using PMSF with GHOST models

  iqtree/iqtree2#459 · Filter by author kr3118 opened on May 3, 2025
  8

• -optlen BFSG with GHOST models

  iqtree/iqtree2#458 · Filter by author kr3118 opened on May 3, 2025
  1

• --polytomy flag unexpected behavior

  iqtree/iqtree2#457 · Filter by author DOH-DEW3303 opened on Apr 25, 2025
  1

• ancestral sequence reconstruction with user tree

  iqtree/iqtree2#448 · Filter by author EHC2019 opened on Apr 8, 2025
  1

• ERROR: STACK TRACE FOR DEBUGGING:

  iqtree/iqtree2#441 · Filter by author xiaoling-lin opened on Mar 28, 2025
  2

• Neither -mset nor -madd accepts MIX{...}

  iqtree/iqtree2#440 · Filter by author HS6986 opened on Mar 28, 2025
  2