iqtree/iqtree2

Issues

• Gamma discretization in AliSim not consistent with tree estimation

  #333 opened 21 days ago by lemmonquiche
  1

• MixtureFinder

  #326 opened 24 days ago by josephhughes
  1

• `-blfix` flag does not prevent reoptimization of branch lengths

  #329 opened 25 days ago by davidcerny
  0

• Output invariant sites position when running +ASC models

  #328 opened a month ago by xiekunwhy
  1

• Matching Gene Trees in Treefile to Alignment File Names

  #327 opened a month ago by simone-says
  0

• `-MFP` fails with parition option `-q`

  #311 opened 2 months ago by roblanf
  2

• ERROR: File not found AA

  #314 opened 2 months ago by wenhaoli-wenhaoli
  4

• Memory issue?

  #321 opened a month ago by brmagalis
  2

• Concordance Analysis Bug - Large Number of Partitions?

  #316 opened 2 months ago by jasongallant
  6

• IQ-TREE multicore version 2.3.6 for Linux x86 64-bit issue with core usage when using -T AUTO and --threads-max combination

  #312 opened 2 months ago by uee9
  1

• IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT

  #307 opened a month ago by z626093820
  1

• ERROR: phylotreepars.cpp:63: void PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*): Assertion `!aln->ordered_pattern.empty()' failed.

  #320 opened 2 months ago by buiguesj
  1

• Build issues on macOS 14.5: ` error: call to 'gettimeofday' is ambiguous`

  #275 opened 2 months ago by corneliusroemer
  1

• CI fails for windows

  #298 opened 2 months ago by corneliusroemer
  0

• Inconsistent results from AU-test

  #308 opened 2 months ago by marybarker
  2

• Model selection time is ~20x slower on the Windows binary vs the Linux binary

  #318 opened 2 months ago by Thernn88
  0

• Segmentation fault with large input matrix

  #303 opened 3 months ago by AryehMiller
  1

• Feature Request: Add option to output nhx instead of iqtree specific newick

  #310 opened 2 months ago by ammaraziz
  0

• EX2 model inconsistent lnl btwn .sitelh and .log files when -blfix specified

  #309 opened 2 months ago by evolbeginner
  0

• ERROR: ratefree.cpp:199: virtual void RateFree::initFromCatMinusOne(Checkpoint&, double): Assertion `fabs(sum_prop + getPInvar() - 1.0) < 0.01' failed.

  #291 opened 3 months ago by yeeus
  2

• IQ-TREE CRASHES WITH SIGNAL ABORTED: 'std::ios_base::failure'

  #304 opened 2 months ago by ClarabellaFantilli
  7

• Error message could be more helpful when file not found

  #302 opened 3 months ago by corneliusroemer
  0

• Why does cmaple cause two versions of iqtree to be available: iqtree and iqtree-aa?

  #299 opened 3 months ago by corneliusroemer
  0

• [Feature Request] Add support for the `--link-exchange-rates` option in the MAST model

  #285 opened 3 months ago by StefanFlaumberg
  2

• Crash due to assertion failure in `PhyloSuperTreePlen::computeFuncDerv`

  #270 opened 4 months ago by davidcerny
  3

• IQTree::optimizeNNI(bool): Assertion `curScore > appliedNNIs.at(0).newloglh - 0.1' failed.

  #230 opened 5 months ago by OliveiraDS-hub
  4

• [BUG] Infinite loop while using BNNI under PMSF model

  #255 opened 3 months ago by StefanFlaumberg
  2

• Web docs (and wiki) are different from cli help

  #287 opened 3 months ago by ammaraziz
  0

• Manual out of date with respect to `-t RANDOM`

  #286 opened 3 months ago by davidcerny
  0

• Despite passing `--output-multifurcating-tree`, resulting tree is bifurcating, when run in cmaple mode

  #283 opened 3 months ago by corneliusroemer
  1

• `--polytomy` flag seems to be ignored when iqtree is using cmaple

  #281 opened 3 months ago by corneliusroemer
  1

• Cmaple CLI args not appearing in help string

  #282 opened 3 months ago by corneliusroemer
  0

• How to reduce verbosity of build logs?

  #278 opened 3 months ago by corneliusroemer
  1

• Consider lowering minimum clang version to 16 for bioconda compatibility

  #277 opened 3 months ago by corneliusroemer
  1

• Paired bootstrap values in a .treefile without having specified -alrt

  #279 opened 4 months ago by davidfbibby
  0

• doc: code not well formatted for macosx compilation guide

  #276 opened 4 months ago by corneliusroemer
  0

• Suggestion: Error instead of warn if `--pathogen-force` is set but cmaple not integrated

  #274 opened 4 months ago by corneliusroemer
  0

• Document in help string that `--nt`/`-c`/`-T`/`--threads` are synonyms, print always `-T` instead of `-nt`

  #273 opened 4 months ago by corneliusroemer
  1

• Bug in writing best_model.nex file

  #272 opened 4 months ago by roblanf
  1

• problem with start the program in command

  #252 opened 4 months ago by zeynab1995
  12

• Error when estimating linked exchangeabilities (GTRpmix)

  #261 opened 4 months ago by mjamy
  4

• not an issue, would like clarification on how to use pmsf

  #262 opened 4 months ago by vmkhot
  0

• Add option to force-unroot input trees

  #251 opened 4 months ago by roblanf
  4

• [Feature Request] Add site-specific rate profile support

  #244 opened 4 months ago by StefanFlaumberg
  3

• ModelFinder doesn't save checkpoint of FreeRate model to model.gz file

  #241 opened 4 months ago by bqminh
  2

• How to obtain the site frequency for each amino acid site under a homogeneous model

  #246 opened 4 months ago by ZQ1126
  1

• Replace the zlib library with zstd or lz4

  #243 opened 4 months ago by bqminh
  0

• Description of -fast option

  #239 opened 5 months ago by ebraun68
  1

• cannot access docs

  #235 opened 5 months ago by blemmond
  1

• IQ-TREE CRASHES WITH SIGNAL ABORTED: -czb threshold specification

  #232 opened 5 months ago by DFornasiero
  4