IQ-TREE 2.4.0 built Feb 7 2025 Input file name: alignment_occupancy50.fasta Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates) Random seed number: 20261027 REFERENCES ---------- To cite IQ-TREE please use: Bui Quang Minh, Heiko A. Schmidt, Olga Chernomor, Dominik Schrempf, Michael D. Woodhams, Arndt von Haeseler, and Robert Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., in press. https://doi.org/10.1093/molbev/msaa015 To cite ModelFinder please use: Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler, and Lars S Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14:587–589. https://doi.org/10.1038/nmeth.4285 Since you used ultrafast bootstrap (UFBoot) please also cite: Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281 SEQUENCE ALIGNMENT ------------------ Input data: 39 sequences with 108 amino-acid sites Number of constant sites: 1 (= 0.925926% of all sites) Number of invariant (constant or ambiguous constant) sites: 1 (= 0.925926% of all sites) Number of parsimony informative sites: 106 Number of distinct site patterns: 108 ModelFinder ----------- Best-fit model according to BIC: LG+G4 List of models sorted by BIC scores: Model LogL AIC w-AIC AICc w-AICc BIC w-BIC LG+G4 -6940.085 14032.170 + 0.668 14409.718 + 1 14236.012 + 0.885 LG+I+G4 -6939.786 14033.573 + 0.331 14433.973 - 5.41e-06 14240.097 + 0.115 WAG+I+G4 -6963.429 14080.858 - 1.79e-11 14481.258 - 2.92e-16 14287.382 - 6.2e-12 WAG+G4 -6966.040 14084.081 - 3.57e-12 14461.629 - 5.34e-12 14287.923 - 4.73e-12 VT+I+G4 -6964.449 14082.897 - 6.45e-12 14483.297 - 1.05e-16 14289.422 - 2.24e-12 VT+G4 -6967.417 14086.834 - 9.02e-13 14464.382 - 1.35e-12 14290.676 - 1.19e-12 LG+F+G4 -6931.249 14052.498 - 2.58e-05 15572.498 - 3.2e-253 14307.301 - 2.93e-16 LG+F+I+G4 -6930.754 14053.509 - 1.55e-05 15746.600 - 5.01e-291 14310.993 - 4.62e-17 JTT+I+G4 -6977.714 14109.429 - 1.12e-17 14509.829 - 1.83e-22 14315.953 - 3.87e-18 JTT+G4 -6981.681 14115.363 - 5.75e-19 14492.911 - 8.61e-19 14319.205 - 7.62e-19 WAG+F+I+G4 -6954.015 14100.030 - 1.23e-15 15793.121 - 3.96e-301 14357.515 - 3.66e-27 WAG+F+G4 -6956.381 14102.761 - 3.14e-16 15622.761 - 3.9e-264 14357.564 - 3.57e-27 VT+F+I+G4 -6962.666 14117.333 - 2.15e-19 15810.424 - 6.93e-305 14374.817 - 6.39e-31 VT+F+G4 -6965.776 14121.551 - 2.61e-20 15641.551 - 3.24e-268 14376.354 - 2.97e-31 JTT+F+I+G4 -6963.906 14119.812 - 6.22e-20 15812.903 - 2.01e-305 14377.296 - 1.85e-31 JTT+F+G4 -6967.709 14125.419 - 3.77e-21 15645.419 - 4.69e-269 14380.221 - 4.29e-32 WAG+I -7033.731 14219.462 - 1.43e-41 14597.011 - 2.14e-41 14423.304 - 1.89e-41 VT+I -7037.507 14227.014 - 3.28e-43 14604.562 - 4.9e-43 14430.856 - 4.34e-43 WAG -7044.555 14239.109 - 7.74e-46 14595.359 - 4.88e-41 14440.269 - 3.92e-45 VT -7049.379 14248.759 - 6.21e-48 14605.009 - 3.92e-43 14449.919 - 3.15e-47 LG+I -7052.465 14256.930 - 1.04e-49 14634.478 - 1.56e-49 14460.772 - 1.38e-49 LG -7060.056 14270.112 - 1.43e-52 14626.362 - 9.05e-48 14471.271 - 7.26e-52 WAG+F+I -7027.027 14244.054 - 6.53e-47 15764.054 - 8.12e-295 14498.856 - 7.43e-58 JTT+I -7072.461 14296.921 - 2.16e-58 14674.470 - 3.24e-58 14500.763 - 2.86e-58 VT+F+I -7031.062 14252.125 - 1.15e-48 15772.125 - 1.44e-296 14506.927 - 1.31e-59 LG+F+I -7033.871 14257.742 - 6.96e-50 15777.742 - 8.66e-298 14512.544 - 7.92e-61 WAG+F -7037.076 14262.152 - 7.68e-51 15635.998 - 5.21e-267 14514.272 - 3.34e-61 LG+F -7040.966 14269.932 - 1.57e-52 15643.778 - 1.07e-268 14522.052 - 6.83e-63 VT+F -7042.400 14272.800 - 3.74e-53 15646.646 - 2.54e-269 14524.920 - 1.63e-63 JTT -7088.929 14327.858 - 4.14e-65 14684.108 - 2.61e-60 14529.018 - 2.1e-64 JTT+F+I -7050.752 14291.504 - 3.25e-57 15811.504 - 4.04e-305 14546.307 - 3.69e-68 JTT+F -7065.152 14318.305 - 4.92e-63 15692.151 - 3.34e-279 14570.425 - 2.14e-73 AIC, w-AIC : Akaike information criterion scores and weights. AICc, w-AICc : Corrected AIC scores and weights. BIC, w-BIC : Bayesian information criterion scores and weights. Plus signs denote the 95% confidence sets. Minus signs denote significant exclusion. SUBSTITUTION PROCESS -------------------- Model of substitution: LG+G4 State frequencies: (model) Model of rate heterogeneity: Gamma with 4 categories Gamma shape alpha: 1.6939 Category Relative_rate Proportion 1 0.2538 0.2500 2 0.6179 0.2500 3 1.0600 0.2500 4 2.0682 0.2500 Relative rates are computed as MEAN of the portion of the Gamma distribution falling in the category. MAXIMUM LIKELIHOOD TREE ----------------------- Log-likelihood of the tree: -6939.7980 (s.e. 184.8168) Unconstrained log-likelihood (without tree): -505.6702 Number of free parameters (#branches + #model parameters): 76 Akaike information criterion (AIC) score: 14031.5961 Corrected Akaike information criterion (AICc) score: 14409.1445 Bayesian information criterion (BIC) score: 14235.4381 Total tree length (sum of branch lengths): 36.1648 Sum of internal branch lengths: 18.3609 (50.7701% of tree length) WARNING: 1 near-zero internal branches (<0.0093) should be treated with caution Such branches are denoted by '**' in the figure below NOTE: Tree is UNROOTED although outgroup taxon 'P29374_PWWP1' is drawn at root Numbers in parentheses are SH-aLRT support (%) / ultrafast bootstrap support (%) +---------P29374_PWWP1 | +**Q4LE39_PWWP1 | | +--O95696_PWWP1 | +--| (16.2/66) | | +--Q9ULD4_PWWP1 | +-------------| (99.9/100) | | +--P55201_PWWP1 | +--| (78.5/73) | | | +--Q9Y6K1_PWWP1 | | | +-----| (93.2/90) | | | | | +**Q9UBC3_PWWP1 | | | | +----| (99.5/100) | | | | +--O88509_PWWP1 | | | +---| (57.9/68) | | | | | +---Q96N64_PWWP1 | | | | +-----------| (99.7/100) | | | | +--Q6NUJ5_PWWP1 | | | +---| (82.7/68) | | | | +-------------Q9P267_PWWP1 | | | +--| (45.9/35) | | | | | +------Q49A26_PWWP1 | | | | | +--| (81.4/70) | | | | | | | +**P51858_PWWP1 | | | | | | | +**| (0/100) | | | | | | | | +**Q8VHK7_PWWP1 | | | | | | | +---------| (99.1/100) | | | | | | | | | +--Q5TGJ6_PWWP1 | | | | | | | | +--| (74.3/73) | | | | | | | | | +--Q7Z4V5_PWWP1 | | | | | | | | | +--| (91.4/98) | | | | | | | | | | +--O75475_PWWP1 | | | | | | | | +--| (96.5/100) | | | | | | | | | +**Q9Y3E1_PWWP1 | | | | | | | | +--| (85.7/99) | | | | | | | | +**Q9JMG7_PWWP1 | | | | | | +----| (91.4/95) | | | | | | +--Q9VAA9_PWWP1 | | | | +--| (26.6/39) | | | | | +--Q96L73_PWWP2 | | | | | +--| (78.3/90) | | | | | | +--O96028_PWWP2 | | | | +-----------------| (100/100) | | | | +--Q9BZ95_PWWP2 | | | +--| (59.8/45) | | | | | +**Q15326_PWWP1 | | | | | +------| (95.6/100) | | | | | | +--Q8R5C8_PWWP1 | | | | +----------| (98.8/99) | | | | +------Q9ULU4_PWWP1 | | | +--| (61.8/16) | | | | | +--Q2TAK8_PWWP1 | | | | | +--| (80.2/93) | | | | | | +--Q5H9M0_PWWP1 | | | | | +--------------------| (99.9/100) | | | | | | +--A0A494C071_PWWP1 | | | | +--| (67.7/22) | | | | | +----------Q9H0M4_PWWP1 | | | | | +--| (56.8/43) | | | | | | +--------------------Q586Y0_PWWP1 | | | | +--| (73.1/32) | | | | +------------------Q504Y3_PWWP1 | | +--| (83.9/66) | | | +---------P52701_PWWP1 | | +--| (84/47) | | | +--------Q96L73_PWWP1 | | | +--| (51.3/45) | | | | +--O96028_PWWP1 | | +-------| (98.3/99) | | +--Q9BZ95_PWWP1 +---------------------| (100/100) | +---------O59676_PWWP1 | +----| (90.1/97) | | +---------O94312_PWWP1 +--| (76.3/77) +-------Q04213_PWWP1 Tree in newick format: (P29374_PWWP1:1.0135028738,Q4LE39_PWWP1:0.0000029539,((((O95696_PWWP1:0.2168794889,Q9ULD4_PWWP1:0.1354491923)16.2/66:0.0344706833,P55201_PWWP1:0.2535530641)99.9/100:1.3617310460,(((((((Q9Y6K1_PWWP1:0.2619386231,(Q9UBC3_PWWP1:0.0000021315,O88509_PWWP1:0.0494517537)99.5/100:0.5009433070)93.2/90:0.5893653139,(Q96N64_PWWP1:0.3806868034,Q6NUJ5_PWWP1:0.0164097730)99.7/100:1.1875777360)57.9/68:0.3803300359,Q9P267_PWWP1:1.3899259590)82.7/68:0.4570684201,((Q49A26_PWWP1:0.6966663504,(((P51858_PWWP1:0.0000010001,Q8VHK7_PWWP1:0.0000010001)0/100:0.0000022613,(Q5TGJ6_PWWP1:0.2715980131,((Q7Z4V5_PWWP1:0.1565053920,O75475_PWWP1:0.1454178141)91.4/98:0.0955930559,(Q9Y3E1_PWWP1:0.0000010001,Q9JMG7_PWWP1:0.0000010001)85.7/99:0.0564705493)96.5/100:0.1453704304)74.3/73:0.0255182559)99.1/100:0.9760886083,Q9VAA9_PWWP1:0.3098048448)91.4/95:0.5011249099)81.4/70:0.3252078978,((Q96L73_PWWP2:0.2845536766,O96028_PWWP2:0.2235469616)78.3/90:0.1426726786,Q9BZ95_PWWP2:0.1540598565)100/100:1.7551241810)26.6/39:0.0914787735)45.9/35:0.1739519875,((Q15326_PWWP1:0.0000022123,Q8R5C8_PWWP1:0.0099990898)95.6/100:0.6655852194,Q9ULU4_PWWP1:0.7464481090)98.8/99:1.0465595680)59.8/45:0.1681653911,(((Q2TAK8_PWWP1:0.2738440926,Q5H9M0_PWWP1:0.1896026525)80.2/93:0.2116224798,A0A494C071_PWWP1:0.3196006242)99.9/100:2.0225690630,((Q9H0M4_PWWP1:1.1043753328,Q586Y0_PWWP1:2.0335093197)56.8/43:0.1550644859,Q504Y3_PWWP1:1.8574375995)73.1/32:0.1856851963)67.7/22:0.1962923524)61.8/16:0.0868946337,(P52701_PWWP1:0.9655100672,((Q96L73_PWWP1:0.8822743793,O96028_PWWP1:0.2805026918)51.3/45:0.1419808817,Q9BZ95_PWWP1:0.3733617330)98.3/99:0.8007640374)84/47:0.3195609871)83.9/66:0.2924794042)78.5/73:0.3600877196,((O59676_PWWP1:0.9465671461,O94312_PWWP1:0.9865294932)90.1/97:0.4925299699,Q04213_PWWP1:0.8179262551)76.3/77:0.3218729694)100/100:2.1495830930); CONSENSUS TREE -------------- Consensus tree is constructed from 1000 bootstrap trees Log-likelihood of consensus tree: -6940.356834 Robinson-Foulds distance between ML tree and consensus tree: 2 Branches with support >0.000000% are kept (extended consensus) Branch lengths are optimized by maximum likelihood on original alignment Numbers in parentheses are bootstrap supports (%) +---------P29374_PWWP1 | +--Q4LE39_PWWP1 | | +--O95696_PWWP1 | +--| (66) | | +--Q9ULD4_PWWP1 | +-------------| (100) | | +--P55201_PWWP1 | +--| (73) | | | +--Q9Y6K1_PWWP1 | | | +-----| (90) | | | | | +--Q9UBC3_PWWP1 | | | | +----| (100) | | | | +--O88509_PWWP1 | | | +---| (68) | | | | | +--Q96N64_PWWP1 | | | | +-----------| (100) | | | | +--Q6NUJ5_PWWP1 | | | +---| (68) | | | | +-------------Q9P267_PWWP1 | | | +--| (35) | | | | | +------Q49A26_PWWP1 | | | | | +--| (70) | | | | | | | +--P51858_PWWP1 | | | | | | | +--| (100) | | | | | | | | +--Q8VHK7_PWWP1 | | | | | | | +---------| (100) | | | | | | | | | +--Q5TGJ6_PWWP1 | | | | | | | | +--| (73) | | | | | | | | | +--Q7Z4V5_PWWP1 | | | | | | | | | +--| (98) | | | | | | | | | | +--O75475_PWWP1 | | | | | | | | +--| (100) | | | | | | | | | +--Q9Y3E1_PWWP1 | | | | | | | | +--| (99) | | | | | | | | +--Q9JMG7_PWWP1 | | | | | | +----| (95) | | | | | | +--Q9VAA9_PWWP1 | | | | +--| (39) | | | | | +--Q96L73_PWWP2 | | | | | +--| (90) | | | | | | +--O96028_PWWP2 | | | | +-----------------| (100) | | | | +--Q9BZ95_PWWP2 | | | +--| (45) | | | | | +--Q15326_PWWP1 | | | | | +------| (100) | | | | | | +--Q8R5C8_PWWP1 | | | | +----------| (99) | | | | +------Q9ULU4_PWWP1 | | | +--| (16) | | | | | +--Q2TAK8_PWWP1 | | | | | +--| (93) | | | | | | +--Q5H9M0_PWWP1 | | | | | +--------------------| (100) | | | | | | +--A0A494C071_PWWP1 | | | | +--| (22) | | | | | +----------Q9H0M4_PWWP1 | | | | | +--| (43) | | | | | | +---------------------Q586Y0_PWWP1 | | | | +--| (32) | | | | +------------------Q504Y3_PWWP1 | | +--| (66) | | | +----------P52701_PWWP1 | | +--| (47) | | | +-------Q96L73_PWWP1 | | +-------| (99) | | | +--O96028_PWWP1 | | +--| (51) | | +----Q9BZ95_PWWP1 +---------------------| (100) | +---------O59676_PWWP1 | +----| (97) | | +---------O94312_PWWP1 +--| (77) +-------Q04213_PWWP1 Consensus tree in newick format: (P29374_PWWP1:1.0126092374,Q4LE39_PWWP1:0.0000026791,((((O95696_PWWP1:0.2168769822,Q9ULD4_PWWP1:0.1353189606)66:0.0390799391,P55201_PWWP1:0.2495198596)100:1.3681000293,(((((((Q9Y6K1_PWWP1:0.2660156943,(Q9UBC3_PWWP1:0.0000021482,O88509_PWWP1:0.0493993406)100:0.4959861702)90:0.5828902552,(Q96N64_PWWP1:0.3705260304,Q6NUJ5_PWWP1:0.0241961816)100:1.1838299933)68:0.3782385949,Q9P267_PWWP1:1.3852655860)68:0.4412680072,((Q49A26_PWWP1:0.7095965209,(((P51858_PWWP1:0.0000021391,Q8VHK7_PWWP1:0.0000021391)100:0.0000024750,(Q5TGJ6_PWWP1:0.2715846716,((Q7Z4V5_PWWP1:0.1562840007,O75475_PWWP1:0.1452585186)98:0.0953126552,(Q9Y3E1_PWWP1:0.0000021482,Q9JMG7_PWWP1:0.0000021391)99:0.0564974233)100:0.1453374181)73:0.0251678359)100:0.9714683355,Q9VAA9_PWWP1:0.3131148242)95:0.4852594954)70:0.3310935601,((Q96L73_PWWP2:0.2840914007,O96028_PWWP2:0.2231504854)90:0.1415858641,Q9BZ95_PWWP2:0.1549265628)100:1.7378897361)39:0.1234373398)35:0.1711787241,((Q15326_PWWP1:0.0000021391,Q8R5C8_PWWP1:0.0099712043)100:0.6709530373,Q9ULU4_PWWP1:0.7392443974)99:1.0534651729)45:0.1916736956,(((Q2TAK8_PWWP1:0.2730253787,Q5H9M0_PWWP1:0.1899566821)93:0.2176940242,A0A494C071_PWWP1:0.3122720121)100:2.0167113291,((Q9H0M4_PWWP1:1.0947138647,Q586Y0_PWWP1:2.0573558619)43:0.1628725266,Q504Y3_PWWP1:1.8218159840)32:0.1857165867)22:0.1819647193)16:0.0741305424,(P52701_PWWP1:1.0373076744,(Q96L73_PWWP1:0.8018982898,(O96028_PWWP1:0.3037693382,Q9BZ95_PWWP1:0.4868429235)51:0.1055387806)99:0.7823261093)47:0.2558126819)66:0.2988814414)73:0.3416030675,((O59676_PWWP1:0.9487860815,O94312_PWWP1:0.9818589447)97:0.4998922153,Q04213_PWWP1:0.8185201114)77:0.3246481833)100:2.1229033557); ALISIM COMMAND -------------- To simulate an alignment of the same length as the original alignment, using the tree and model parameters estimated from this analysis, you can use the following command: --alisim simulated_MSA -t trees/sensitivity50.treefile -m "LG+G4{1.6939}" --length 108 To mimic the alignment used to produce this analysis, i.e. simulate an alignment of the same length as the original alignment, using the tree and model parameters estimated from this analysis *and* copying the same gap positions as the original alignment, you can use the following command: iqtree -s alignment_occupancy50.fasta --alisim mimicked_MSA To simulate any number of alignments in either of the two commandlines above, use the --num-alignments options, for example mimic 100 alignments you would use the command line: iqtree -s alignment_occupancy50.fasta --alisim mimicked_MSA --num-alignments 100 For more information on using AliSim, please visit: www.iqtree.org/doc/AliSim TIME STAMP ---------- Date and time: Mon Oct 26 13:00:34 2026 Total CPU time used: 664.994733 seconds (0h:11m:4s) Total wall-clock time used: 358.0719151 seconds (0h:5m:58s)