iqtree iqtree2 issues - Githubissues

iqtree / iqtree2

NEW location of IQ-TREE software for efficient phylogenomic software by maximum likelihood http://www.iqtree.org

GNU General Public License v2.0

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issues

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AliSim Outputs Identical Sequences in Simulated Alignments

#352 simone-says closed 5 days ago
0
Fix auto-detection of binary data

#350 davidcerny closed 4 days ago
0
Parameter -o for setting outgroup is not working and I'm getting a long branch for the first species (IQTree2.3.4)

#349 badiaclara closed 1 week ago
1
adding -mem to partitioned models like -S search

#346 drelo opened 1 week ago
0
Wrong number of states detected for a morphological alignment

#344 davidcerny closed 4 days ago
8
Support label missing when two children of a node have zero length

#343 terrycojones closed 1 week ago
8
Show meaningful error when partition names include illegal characters

#342 roblanf opened 2 weeks ago
0
ntmax not obeyed

#340 digitalwright opened 2 weeks ago
7
Alisim --num-alignments differences between first and subsequent alignments

#338 elsemikk closed 2 weeks ago
4
Error when computing gcf on species tree.

#337 hutumpyancha closed 1 week ago
5
Could an option be added to tell iqtree2 not to change sequence identifiers?

#335 terrycojones opened 3 weeks ago
2
Alisim mpi

#334 trongnhanuit opened 1 month ago
3
Gamma discretization in AliSim not consistent with tree estimation

#333 lemmonquiche opened 1 month ago
3
Onnxupdate new schedluing

#332 Hashara closed 1 month ago
0
Onnxupdate

#331 Hashara closed 1 month ago
0
`-blfix` flag does not prevent reoptimization of branch lengths

#329 davidcerny opened 1 month ago
0
Output invariant sites position when running +ASC models

#328 xiekunwhy closed 3 weeks ago
1
Matching Gene Trees in Treefile to Alignment File Names

#327 simone-says opened 1 month ago
1
MixtureFinder

#326 josephhughes closed 1 month ago
1
Memory issue?

#321 brmagalis closed 1 month ago
2
ERROR: phylotreepars.cpp:63: void PhyloTree::computePartialParsimonyFast(PhyloNeighbor*, PhyloNode*): Assertion `!aln->ordered_pattern.empty()' failed.

#320 buiguesj opened 2 months ago
1
Model selection time is ~20x slower on the Windows binary vs the Linux binary

#318 Thernn88 opened 2 months ago
0
Concordance Analysis Bug - Large Number of Partitions?

#316 jasongallant opened 2 months ago
6
ERROR: File not found AA

#314 wenhaoli-wenhaoli opened 2 months ago
4
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 uee9 opened 2 months ago
4
`-MFP` fails with parition option `-q`

#311 roblanf opened 2 months ago
2
Feature Request: Add option to output nhx instead of iqtree specific newick

#310 ammaraziz opened 2 months ago
0
EX2 model inconsistent lnl btwn .sitelh and .log files when -blfix specified

#309 evolbeginner opened 2 months ago
0
Inconsistent results from AU-test

#308 marybarker opened 2 months ago
2
IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT

#307 z626093820 closed 1 month ago
1
IQ-TREE CRASHES WITH SIGNAL ABORTED: 'std::ios_base::failure'

#304 ClarabellaFantilli closed 2 months ago
8
Segmentation fault with large input matrix

#303 AryehMiller opened 3 months ago
2
Error message could be more helpful when file not found

#302 corneliusroemer opened 3 months ago
0
Why does cmaple cause two versions of iqtree to be available: iqtree and iqtree-aa?

#299 corneliusroemer opened 3 months ago
0
CI fails for windows

#298 corneliusroemer closed 2 months ago
0
chore(ci): make windows ci work by using c++14 for windows ci

#297 corneliusroemer closed 2 months ago
0
Onnxupdate

#296 Hashara closed 3 months ago
0
Replace TravisCI badge with GitHub Actions badge

#292 ryneches closed 3 months ago
0
ERROR: ratefree.cpp:199: virtual void RateFree::initFromCatMinusOne(Checkpoint&, double): Assertion `fabs(sum_prop + getPInvar() - 1.0) < 0.01' failed.

#291 yeeus opened 3 months ago
3
Onnxupdate

#289 Hashara closed 3 months ago
0
Onnxupdate

#288 Hashara closed 3 months ago
0
Web docs (and wiki) are different from cli help

#287 ammaraziz opened 3 months ago
0
Manual out of date with respect to `-t RANDOM`

#286 davidcerny opened 3 months ago
0
[Feature Request] Add support for the `--link-exchange-rates` option in the MAST model

#285 StefanFlaumberg opened 3 months ago
2
Version 2.3.6

#284 thomaskf closed 3 months ago
0
Despite passing `--output-multifurcating-tree`, resulting tree is bifurcating, when run in cmaple mode

#283 corneliusroemer opened 3 months ago
1
Cmaple CLI args not appearing in help string

#282 corneliusroemer opened 3 months ago
0
`--polytomy` flag seems to be ignored when iqtree is using cmaple

#281 corneliusroemer opened 3 months ago
1
doc: Add supported platforms shield to readme

#280 corneliusroemer closed 3 months ago
0
Paired bootstrap values in a .treefile without having specified -alrt

#279 davidfbibby opened 4 months ago
0