iqtree/iqtree2

Issues

• ntmax not obeyed

  #340 opened 2 months ago by digitalwright
  7

• Support label missing when two children of a node have zero length

  #343 opened 2 months ago by terrycojones
  8

• Could an option be added to tell iqtree2 not to change sequence identifiers?

  #335 opened 2 months ago by terrycojones
  2

• 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 4 months ago by uee9
  4

• Wrong number of states detected for a morphological alignment

  #344 opened a month ago by davidcerny
  8

• AliSim Outputs Identical Sequences in Simulated Alignments

  #352 opened a month ago by simone-says
  0

• Parameter -o for setting outgroup is not working and I'm getting a long branch for the first species (IQTree2.3.4)

  #349 opened a month ago by badiaclara
  1

• adding -mem to partitioned models like -S search

  #346 opened a month ago by drelo
  0

• Error when computing gcf on species tree.

  #337 opened 2 months ago by hutumpyancha
  5

• Show meaningful error when partition names include illegal characters

  #342 opened 2 months ago by roblanf
  0

• Alisim --num-alignments differences between first and subsequent alignments

  #338 opened 2 months ago by elsemikk
  4

• Segmentation fault with large input matrix

  #303 opened 4 months ago by AryehMiller
  2

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

  #291 opened 5 months ago by yeeus
  3

• Output invariant sites position when running +ASC models

  #328 opened 2 months ago by xiekunwhy
  1

• Matching Gene Trees in Treefile to Alignment File Names

  #327 opened 2 months ago by simone-says
  1

• Gamma discretization in AliSim not consistent with tree estimation

  #333 opened 2 months ago by lemmonquiche
  3

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

  #304 opened 4 months ago by ClarabellaFantilli
  8

• MixtureFinder

  #326 opened 2 months ago by josephhughes
  1

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

  #329 opened 2 months ago by davidcerny
  0

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

  #311 opened 4 months ago by roblanf
  2

• ERROR: File not found AA

  #314 opened 4 months ago by wenhaoli-wenhaoli
  4

• Memory issue?

  #321 opened 3 months ago by brmagalis
  2

• Concordance Analysis Bug - Large Number of Partitions?

  #316 opened 3 months ago by jasongallant
  6

• IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT

  #307 opened 3 months ago by z626093820
  1

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

  #320 opened 3 months ago by buiguesj
  1

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

  #275 opened 3 months ago by corneliusroemer
  1

• CI fails for windows

  #298 opened 3 months ago by corneliusroemer
  0

• Inconsistent results from AU-test

  #308 opened 4 months ago by marybarker
  2

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

  #318 opened 3 months ago by Thernn88
  0

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

  #310 opened 4 months ago by ammaraziz
  0

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

  #309 opened 4 months ago by evolbeginner
  0

• Error message could be more helpful when file not found

  #302 opened 4 months ago by corneliusroemer
  0

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

  #299 opened 4 months ago by corneliusroemer
  0

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

  #285 opened 5 months ago by StefanFlaumberg
  2

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

  #270 opened 5 months ago by davidcerny
  3

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

  #255 opened 5 months ago by StefanFlaumberg
  2

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

  #287 opened 5 months ago by ammaraziz
  0

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

  #286 opened 5 months ago by davidcerny
  0

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

  #283 opened 5 months ago by corneliusroemer
  1

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

  #281 opened 5 months ago by corneliusroemer
  1

• Cmaple CLI args not appearing in help string

  #282 opened 5 months ago by corneliusroemer
  0

• How to reduce verbosity of build logs?

  #278 opened 5 months ago by corneliusroemer
  1

• Consider lowering minimum clang version to 16 for bioconda compatibility

  #277 opened 5 months ago by corneliusroemer
  1

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

  #279 opened 5 months ago by davidfbibby
  0

• doc: code not well formatted for macosx compilation guide

  #276 opened 5 months ago by corneliusroemer
  0

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

  #274 opened 5 months ago by corneliusroemer
  0

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

  #273 opened 5 months ago by corneliusroemer
  1

• Bug in writing best_model.nex file

  #272 opened 5 months ago by roblanf
  1

• Error when estimating linked exchangeabilities (GTRpmix)

  #261 opened 6 months ago by mjamy
  4

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

  #262 opened 6 months ago by vmkhot
  0