BUG: When including duplicate taxon in constraint tree, misleading/incorrect error thrown

[corneliusroemer]

I figured out what the root cause was. The issue is with the error message not with the rest of the software - but I'm leaving the issue as is. See the first command for an explanation of what I found

I use constraint trees to make the Nextclade reference trees, see e.g. https://nextstrain.org/staging/nextclade/sars-cov-2

Without constraint trees, the large amount of homoplasy causes the tree to be wrong. This is an ideal use case for constraint trees.

Things have been working well - until today.

When I increased the size of the constraint tree to now 83 sequences, suddenly I get errors that are wrong - in the sense that they claim something that is not true.

:ERROR: Alignment sequence BA.2.38.2 does not appear in the tree
ERROR: Tree taxa and alignment sequence do not match (see above)

This is the command I run with data attached:
iqtree-2.2.0.7-MacOSX/bin/iqtree2 -s masked_masked-delim.fasta.txt -m GTR -g constraint-2.nwk.txt -czb -redo

masked_masked-delim.fasta.txt
constraint-2.nwk.txt

When I run iqtree2 without constraint tree, all works well:
iqtree-2.2.0.7-MacOSX/bin/iqtree2 -s masked_masked-delim.fasta.txt -m GTR -czb -redo

When I use my previous constraint tree - all works well:
iqtree-2.2.0.7-MacOSX/bin/iqtree2 -s masked_masked-delim.fasta -m GTR -g constraint-old.nwk -czb -redo
constraint-old.nwk.txt

So something is really wrong with the software here - it appears that something fails during the parsimony tree by addition stage. No clue why.

The bug is kind of critical for the ability to produce decent trees for Nextclade so I would very much appreciate if you could have a look at addressing this. Or am I doing something wrong? I hope you can reproduce with the above commands.

I'm running this on an M1 Mac - but this shouldn't really matter?

@thomaskf @bqminh

To convince yourself that the error message is nonsense, have a look at the log, the sequence that's purportedly missing has actually passed QC:

Unfold for logs

IQ-TREE multicore version 2.2.0.7 COVID-edition for Mac OS X 64-bit built Aug 31 2022
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams, Ly Trong Nhan.

Host:    kb-kbbp01-plm98.pz.unibas.ch (SSE4.2, 32 GB RAM)
Command: iqtree-2.2.0.7-MacOSX/bin/iqtree2 -s masked_masked-delim.fasta -m GTR -g constraint-2.nwk -czb -redo
Seed:    765928 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Sat Sep  3 20:00:36 2022
Kernel:  SSE2 - 1 threads (10 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 10 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading alignment file masked_masked-delim.fasta ... Fasta format detected
Reading fasta file: done in 0.337708 secs using 97.93% CPU
Alignment most likely contains DNA/RNA sequences
Constructing alignment: done in 0.050678 secs using 89.05% CPU
WARNING: 203 sites contain only gaps or ambiguous characters.
Alignment has 255 sequences with 29903 columns, 553 distinct patterns
143 parsimony-informative, 449 singleton sites, 29311 constant sites
           Gap/Ambiguity  Composition  p-value
Analyzing sequences: done in 0.000226974 secs using 92.96% CPU
   1  BA.2.1       0.86%    passed    100.00%
   2  BA.2         0.68%    passed     99.89%
   3  BA.2.10.1    0.86%    passed    100.00%
   4  BA.2.10      0.86%    passed    100.00%
   5  BA.2.10.2    0.86%    passed    100.00%
   6  BA.2.10.3    0.86%    passed     99.99%
   7  BA.2.10.4    0.92%    passed     99.91%
   8  BA.2.11      0.85%    passed    100.00%
   9  BA.2.12      0.86%    passed    100.00%
  10  BA.2.12.2    0.86%    passed    100.00%
  11  BA.2.12.1    0.86%    passed    100.00%
  12  BA.2.13.1    0.86%    passed    100.00%
  13  BA.2.14      0.77%    passed     99.99%
  14  BA.2.13      0.84%    passed    100.00%
  15  BA.2.15      0.86%    passed    100.00%
  16  BA.2.16      0.88%    passed    100.00%
  17  BA.2.18      0.86%    passed    100.00%
  18  BA.2.19      0.86%    passed    100.00%
  19  BA.2.17      0.86%    passed    100.00%
  20  BA.2.2       0.86%    passed    100.00%
  21  BA.2.2.1     0.86%    passed    100.00%
  22  BA.2.20      0.86%    passed    100.00%
  23  BA.2.21      0.86%    passed    100.00%
  24  BA.2.24      0.86%    passed    100.00%
  25  BA.2.23.1    0.86%    passed    100.00%
  26  BA.2.22      0.86%    passed    100.00%
  27  BA.2.23      0.86%    passed    100.00%
  28  BA.2.25.1    0.86%    passed    100.00%
  29  BA.2.25      0.86%    passed    100.00%
  30  BA.2.26      0.85%    passed    100.00%
  31  BA.2.27      0.86%    passed    100.00%
  32  BA.2.29      0.86%    passed    100.00%
  33  BA.2.3       0.86%    passed    100.00%
  34  BA.2.28      0.86%    passed    100.00%
  35  BA.2.3.10    0.86%    passed    100.00%
  36  BA.2.3.11    0.86%    passed    100.00%
  37  BA.2.3.1     0.86%    passed    100.00%
  38  BA.2.3.12    0.86%    passed    100.00%
  39  BA.2.3.13    0.86%    passed    100.00%
  40  BA.2.3.14    0.86%    passed    100.00%
  41  BA.2.3.16    0.86%    passed    100.00%
  42  BA.2.3.15    0.86%    passed    100.00%
  43  BA.2.3.19    0.83%    passed    100.00%
  44  BA.2.3.18    0.86%    passed    100.00%
  45  BA.2.3.17    0.86%    passed    100.00%
  46  BA.2.3.2     0.86%    passed    100.00%
  47  BA.2.3.4     0.86%    passed    100.00%
  48  BA.2.3.20    0.86%    passed     99.94%
  49  BA.2.3.5     0.86%    passed    100.00%
  50  BA.2.3.7     0.86%    passed    100.00%
  51  BA.2.3.8     0.86%    passed     99.99%
  52  BA.2.3.6     0.86%    passed    100.00%
  53  BA.2.3.9     0.86%    passed    100.00%
  54  BA.2.30      0.86%    passed    100.00%
  55  BA.2.31      0.86%    passed    100.00%
  56  BA.2.32      0.86%    passed    100.00%
  57  BA.2.33      0.77%    passed     99.98%
  58  BA.2.34      0.86%    passed    100.00%
  59  BA.2.35      0.86%    passed    100.00%
  60  BA.2.36      0.86%    passed    100.00%
  61  BA.2.37      0.86%    passed    100.00%
  62  BA.2.38      0.85%    passed    100.00%
  63  BA.2.38.1    0.85%    passed     99.99%
  64  BA.2.38.2    0.85%    passed    100.00%
  65  BA.2.38.3    0.87%    passed     99.99%
  66  BA.2.4       0.86%    passed    100.00%
  67  BA.2.39      0.86%    passed    100.00%
  68  BA.2.40      0.77%    passed     99.98%
  69  BA.2.40.1    0.86%    passed    100.00%
  70  BA.2.41      0.86%    passed    100.00%
  71  BA.2.42      0.86%    passed    100.00%
  72  BA.2.43      0.81%    passed    100.00%
  73  BA.2.44      0.77%    passed     99.97%
  74  BA.2.46      0.86%    passed    100.00%
  75  BA.2.45      0.86%    passed    100.00%
  76  BA.2.47      0.77%    passed     99.99%
  77  BA.2.48      0.85%    passed    100.00%
  78  BA.2.5       0.86%    passed    100.00%
  79  BA.2.49      0.86%    passed    100.00%
  80  BA.2.50      0.86%    passed    100.00%
  81  BA.2.51      0.77%    passed     99.98%
  82  BA.2.53      0.77%    passed     99.99%
  83  BA.2.52      0.77%    passed     99.97%
  84  BA.2.54      0.86%    passed    100.00%
  85  BA.2.55      0.86%    passed    100.00%
  86  BA.2.56      0.86%    passed    100.00%
  87  BA.2.56.1    0.86%    passed    100.00%
  88  BA.2.57      0.86%    passed    100.00%
  89  BA.2.6       0.82%    passed    100.00%
  90  BA.2.59      0.86%    passed    100.00%
  91  BA.2.58      0.86%    passed    100.00%
  92  BA.2.60      0.86%    passed     99.99%
  93  BA.2.63      0.86%    passed    100.00%
  94  BA.2.61      0.86%    passed    100.00%
  95  BA.2.64      0.86%    passed    100.00%
  96  BA.2.65      0.86%    passed    100.00%
  97  BA.2.66      0.77%    passed     99.99%
  98  BA.2.62      0.86%    passed    100.00%
  99  BA.2.67      0.86%    passed    100.00%
 100  BA.2.68      0.77%    passed     99.99%
 101  BA.2.69      0.86%    passed    100.00%
 102  BA.2.7       0.86%    passed    100.00%
 103  BA.2.70      0.77%    passed     99.99%
 104  BA.2.73      0.86%    passed    100.00%
 105  BA.2.71      0.77%    passed     99.97%
 106  BA.2.72      0.86%    passed    100.00%
 107  BA.2.75      0.77%    passed     99.99%
 108  BA.2.74      0.77%    passed     99.99%
 109  BA.2.75.2    0.77%    passed    100.00%
 110  BA.2.75.1    0.86%    passed    100.00%
 111  BA.2.75.3    0.86%    passed    100.00%
 112  BA.2.75.4    0.77%    passed     99.99%
 113  BA.2.75.5    0.77%    passed     99.99%
 114  BA.2.75.6    0.77%    passed     99.99%
 115  BA.2.75.7    0.86%    passed    100.00%
 116  BA.2.76.1    0.86%    passed     99.99%
 117  BA.2.76      0.86%    passed    100.00%
 118  BA.2.77      0.79%    passed     99.99%
 119  BA.2.76.2    0.86%    passed     99.99%
 120  BA.2.78      0.85%    passed    100.00%
 121  BA.2.8       0.86%    passed    100.00%
 122  BA.2.79.1    0.86%    passed     99.99%
 123  BA.2.80      0.77%    passed     99.98%
 124  BA.2.79      0.86%    passed    100.00%
 125  BA.2.81      0.86%    passed    100.00%
 126  BA.2.9       0.77%    passed     99.98%
 127  BA.2.9.2     0.86%    passed    100.00%
 128  BA.2.9.3     0.86%    passed    100.00%
 129  BA.2.82      0.86%    passed    100.00%
 130  BA.2.9.4     0.86%    passed     99.99%
 131  BA.2.9.5     0.86%    passed    100.00%
 132  BA.2.9.1     0.86%    passed    100.00%
 133  BA.3         0.86%    passed     99.87%
 134  BA.4         0.99%    passed    100.00%
 135  BA.4.1       0.91%    passed    100.00%
 136  BA.2.9.6     0.77%    passed     99.99%
 137  BA.4.1.1     0.91%    passed    100.00%
 138  BA.4.1.2     0.82%    passed     99.98%
 139  BA.4.1.4     0.91%    passed    100.00%
 140  BA.4.1.5     0.91%    passed    100.00%
 141  BA.4.1.6     0.91%    passed    100.00%
 142  BA.4.1.3     0.91%    passed    100.00%
 143  BA.4.1.8     0.93%    passed     99.99%
 144  BA.4.1.9     0.91%    passed     99.99%
 145  BA.4.2       0.91%    passed    100.00%
 146  BA.4.3       0.91%    passed    100.00%
 147  BA.4.4       0.91%    passed    100.00%
 148  BA.4.1.7     0.91%    passed    100.00%
 149  BA.4.5       0.91%    passed    100.00%
 150  BA.4.7       0.91%    passed     99.99%
 151  BA.4.8       0.88%    passed    100.00%
 152  BA.5         0.96%    passed    100.00%
 153  BA.5.1       0.88%    passed    100.00%
 154  BA.5.1.1     0.88%    passed    100.00%
 155  BA.5.1.10    0.88%    passed    100.00%
 156  BA.4.6       0.91%    passed    100.00%
 157  BA.5.1.11    0.88%    passed    100.00%
 158  BA.5.1.12    0.88%    passed    100.00%
 159  BA.5.1.13    0.88%    passed    100.00%
 160  BA.5.1.15    0.88%    passed    100.00%
 161  BA.5.1.16    0.88%    passed    100.00%
 162  BA.5.1.17    0.88%    passed    100.00%
 163  BA.5.1.14    0.88%    passed    100.00%
 164  BA.5.1.18    0.88%    passed     99.99%
 165  BA.5.1.2     0.88%    passed     99.99%
 166  BA.5.1.3     0.88%    passed     99.99%
 167  BA.5.1.4     0.88%    passed     99.99%
 168  BA.5.1.6     0.88%    passed     99.99%
 169  BA.5.1.5     0.88%    passed    100.00%
 170  BA.5.1.7     0.88%    passed    100.00%
 171  BA.5.1.8     0.88%    passed     99.99%
 172  BA.5.1.9     0.88%    passed    100.00%
 173  BA.5.10      0.88%    passed    100.00%
 174  BA.5.2       0.88%    passed    100.00%
 175  BA.5.2.1     0.88%    passed    100.00%
 176  BA.5.2.10    0.88%    passed     99.99%
 177  BA.5.2.11    0.88%    passed     99.97%
 178  BA.5.2.3     0.88%    passed     99.98%
 179  BA.5.2.12    0.88%    passed     99.99%
 180  BA.5.2.2     0.88%    passed     99.99%
 181  BA.5.2.4     0.88%    passed    100.00%
 182  BA.5.2.5     0.88%    passed    100.00%
 183  BA.5.2.6     0.88%    passed     99.99%
 184  BA.5.2.8     0.88%    passed     99.99%
 185  BA.5.2.7     0.88%    passed     99.99%
 186  BA.5.2.9     0.88%    passed    100.00%
 187  BA.5.3.1     0.88%    passed    100.00%
 188  BA.5.3.3     1.09%    passed     99.83%
 189  BA.5.3       0.88%    passed    100.00%
 190  BA.5.3.2     0.88%    passed     99.99%
 191  BA.5.5       0.88%    passed    100.00%
 192  BA.5.3.4     0.88%    passed    100.00%
 193  BA.5.5.2     0.88%    passed    100.00%
 194  BA.5.5.1     0.88%    passed    100.00%
 195  BA.5.5.3     0.88%    passed    100.00%
 196  BA.5.6       0.88%    passed    100.00%
 197  BA.5.6.1     0.88%    passed    100.00%
 198  BA.5.6.2     0.88%    passed    100.00%
 199  BA.5.7       0.88%    passed     99.99%
 200  BA.5.8       0.88%    passed    100.00%
 201  BA.5.9       0.88%    passed    100.00%
 202  BE.1         0.88%    passed     99.99%
 203  BE.1.2       0.88%    passed     99.99%
 204  BE.1.1.1     0.88%    passed     99.99%
 205  BE.1.1       0.88%    passed     99.99%
 206  BE.1.3       0.91%    passed     99.98%
 207  BE.3         0.88%    passed    100.00%
 208  BE.2         0.88%    passed    100.00%
 209  BF.1         0.88%    passed    100.00%
 210  BF.1.1       0.88%    passed    100.00%
 211  BF.11        0.88%    passed    100.00%
 212  BF.10        0.88%    passed    100.00%
 213  BF.12        0.88%    passed    100.00%
 214  BF.13        0.88%    passed     99.99%
 215  BF.14        0.79%    passed     99.94%
 216  BF.16        0.88%    passed     99.99%
 217  BF.15        0.88%    passed    100.00%
 218  BF.18        0.88%    passed    100.00%
 219  BF.2         0.88%    passed    100.00%
 220  BF.17        0.88%    passed    100.00%
 221  BF.19        0.88%    passed     99.99%
 222  BF.21        0.88%    passed     99.99%
 223  BF.20        0.88%    passed     99.99%
 224  BF.3         0.88%    passed    100.00%
 225  BF.22        0.88%    passed     99.99%
 226  BF.4         0.88%    passed    100.00%
 227  BF.3.1       0.88%    passed    100.00%
 228  BF.5         0.88%    passed     99.99%
 229  BF.6         0.88%    passed    100.00%
 230  BF.7         0.88%    passed    100.00%
 231  BF.8         0.88%    passed    100.00%
 232  BF.9         0.88%    passed    100.00%
 233  BG.1         0.86%    passed    100.00%
 234  BG.2         0.86%    passed     99.96%
 235  BG.3         0.86%    passed    100.00%
 236  BG.4         0.86%    passed     99.99%
 237  BG.5         0.86%    passed    100.00%
 238  BG.6         0.86%    passed    100.00%
 239  BH.1         0.89%    passed    100.00%
 240  BJ.1         0.87%    passed     99.91%
 241  BK.1         0.88%    passed    100.00%
 242  BL.2         0.86%    passed     99.99%
 243  BL.3         0.86%    passed     99.99%
 244  BL.1         0.86%    passed    100.00%
 245  BL.4         0.86%    passed     99.98%
 246  BM.1         0.86%    passed    100.00%
 247  BM.1.1       0.86%    passed    100.00%
 248  BM.2         0.86%    passed     99.99%
 249  BN.1         0.77%    passed     99.99%
 250  BM.3         0.86%    passed     99.99%
 251  BQ.1         0.88%    passed     99.99%
 252  BP.1         0.88%    passed     99.96%
 253  BN.2         0.77%    passed     99.98%
 254  BN.2.1       0.86%    passed    100.00%
 255  BR.1         0.86%    passed     99.99%
****  TOTAL        0.86%  0 sequences failed composition chi2 test (p-value<5%; df=3)
Reading constraint tree constraint-2.nwk...
NOTE: BA.4.1.1 is identical to BA.4.1 but kept for subsequent analysis
Checking for duplicate sequences: done in 0.000617981 secs using 83.98% CPU
Creating fast initial parsimony tree by random order stepwise addition...
(BA.3,BA.2,(BA.2.19,((BA.2.70,(BA.2.27,(BA.2.64,(BA.2.58,((BA.2.56,BA.2.56.1),((BA.2.49,BA.2.50),(BA.2.39,(BA.2.61,(BA.2.24,((BA.2.54,BA.2.48),(BA.2.30,((BA.2.23,BA.2.23.1),(BA.2.28,(BA.2.41,(BA.2.32,(BA.2.63,(BA.2.20,((BA.2.42,(BA.2.82,BA.2.55)),(BA.2.60,((BA.2.35,BA.2.33),(BA.2.43,((BA.2.59,BA.2.46),(BA.2.65,(BA.2.29,(BA.2.26,(BA.2.62,(BA.2.31,((((BA.2.10.3,(BA.2.10.4,((BA.2.10.1,BJ.1),BA.2.10))),BA.2.10.2)BA.2.10,(BA.2.1,(BA.2.5,((BA.2.40,BA.2.40.1),((BA.2.66,(BA.2.57,(BA.2.21,(BA.2.37,(((BA.2.74,((BA.2.76.2,BA.2.76.1),BA.2.76)),(BA.2.68,((BA.2.73,((((BM.3,(BM.2,BA.2.75.3)),(BM.1,BM.1.1)),((BA.2.75.4,BR.1),(BA.2.75.6,((((BL.2,BL.3)22612T,(BL.1,BA.2.75.1)),BL.4),(((BA.2.75.5,BN.1),(BN.2,BN.2.1)),BA.2.75))))),(BA.2.75.2,BA.2.75.7))),(BA.2.17,(BA.2.78,(((BA.2.38.3,BH.1),(BA.2.38.2,(BA.2.38,BA.2.38.1))),(BA.2.67,(BA.2.79.1,BA.2.79)))))))),((BA.2.12,BA.2.12.2),(BA.2.12.1,(BG.5,(BG.6,((BG.3,(BG.4,BG.1)),BG.2)22C)))))25416)))),(BA.2.4,((BA.2.11,BA.2.77),(BA.2.18,((BA.2.3.17,(BA.2.3.13,(BA.2.3.18,(BA.2.3.6,(BA.2.3.15,(BA.2.3.2,(BA.2.3.9,(BA.2.3.10,(BA.2.3.19,(BA.2.3.11,(BA.2.3.8,(BA.2.3.5,(BA.2.3.4,(BA.2.3.7,(BA.2.3.14,(BA.2.3.12,(BA.2.3.1,(((BA.2.3,BA.2.3.20),(BA.2.3.16,BP.1))BA.2.3,BA.2.3)))))))))))))))))),((BA.2.53,(BA.2.52,(BA.2.69,(BA.2.47,(BA.2.45,(BA.2.51,(BA.2.22,(BA.2.80,(BA.2.34,((BA.2.71,(BA.2.7,(BA.2.6,(BA.2.14,((BA.2.25,BA.2.25.1),(BA.2.36,(BA.2.72,(((BA.2.9,(BA.2.9.3,(BA.2.9.2,((BA.2.9.6,BA.2.9.1),BA.2.9.4)))),BA.2.9.5),(BA.2.44,(BA.2.13,BA.2.13.1)))))))))),BA.2.81)22792))))))))),(BA.2.2.1,BA.2.2))))))))))),BA.2.8)9866))))))))))))))))))))))))))),(((BA.4.8,(BA.4.2,((BA.4.6,(BA.4.3,(BA.4.5,(BA.4.7,BA.4.4)))),(BA.4,(BA.4.1.4,((BA.4.1.9,BA.4.1.8),(BA.4.1.3,(BA.4.1.5,(BA.4.1.6,((BA.4.1,BA.4.1.1),(BA.4.1.7,BA.4.1.2))))))))))),((BA.5.6.1,(BA.5.6,BA.5.6.2)),((BA.5.7,BA.5.8),(BA.5.9,((BA.5.3.3,((BA.5.3.4,BA.5.3.2),((BE.3,(BA.5.3.1,(BE.2,(BE.1,(BE.1.3,(BE.1.2,((BQ.1,BE.1.1.1),BE.1.1))))))),BA.5.3))),((BA.5.5.2,(BA.5.5,(BA.5.5.3,BA.5.5.1))),((BA.5.10,(BA.5.2,((BF.17,(BF.19,(BF.14,(BF.4,(BF.6,(BA.5.2.1,(BF.12,(BF.8,((BF.9,((BF.1.1,BF.1),(BF.2,((BF.3.1,BF.3),(BF.10,((BF.13,(BF.16,BF.22)),(BF.21,(BF.15,BF.20)))))))),((BF.11,BF.7),BF.18)))))))))),(BA.5.2.9,(BA.5.2.4,((BA.5.2.10,(BA.5.2.2,(BA.5.2.8,(BA.5.2.12,(BA.5.2.3,(BA.5.2.6,(BA.5.2.11,BA.5.2.7))))))),BA.5.2.5)))))),((BA.5.1.14,(BA.5.1.8,(BA.5.1,(BA.5.1.3,(BA.5.1.18,(BA.5.1.12,(BA.5.1.6,(BA.5.1.13,(BA.5.1.7,(BA.5.1.5,((BA.5.1.1,BA.5.1.9),(BA.5.1.11,((BA.5.1.10,BK.1),(BA.5.1.16,(BA.5.1.2,(BA.5.1.4,(BA.5.1.17,BA.5.1.15))))))))))))))))),BA.5)))))))),(BA.2.15,BA.2.16)))));
ERROR: Alignment sequence BF.5 does not appear in the tree
ERROR: Tree taxa and alignment sequence do not match (see above)

Same bug happens with version 2.1.4 - so this seems to be a long standing issue.

The "missing" sequence differs every time:

It also doesn't work in 1.6.12 - but I'm not sure whether this is expected or not:

[corneliusroemer]

Ok, I've figured it out 🎉

The root cause is me - but the error message is misleading/false.

I included one sample twice in the constraint tree: BA.2.3

When removing the duplicate element from the constraint tree, it all works.

So what needs to be changed is that when parsing the constraint tree you throw an error: duplicate taxa detected in constraint tree, named BA.2.3

[corneliusroemer]

Notably, the error is thrown not even naming which sequence is duplicate - misleading the user.

I just ran into this again - as I'm hand-writing a pretty large .nwk so these issues are bound to happen. Would be great if there was a good constraint tree nwk validator.

[bqminh]

I'll look into this, thanks for your patience. Btw IQ-TREE back then didn't support Mac ARM (it does now with v2.3.X). So how could you run IQ-TREE back then?

[corneliusroemer]

Thanks for your work on IQtree, my many issue reports should be seen as testament to the importance of IQtree!

Btw IQ-TREE back then didn't support Mac ARM (it does now with v2.3.X). So how could you run IQ-TREE back then?
Rosetta 2 emulation allows running x86 binaries on arm - it's just about 2x slower.