IQ-TREE 2.4.0 built Feb 7 2025 Input file name: alignment_masked.fasta Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates) Random seed number: 20261026 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 78 amino-acid sites Number of constant sites: 1 (= 1.28205% of all sites) Number of invariant (constant or ambiguous constant) sites: 1 (= 1.28205% of all sites) Number of parsimony informative sites: 76 Number of distinct site patterns: 78 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 -4939.797 10031.594 + 0.719 21735.594 - 0 10210.703 + 0.893 LG+I+G4 -4939.736 10033.473 + 0.281 22045.473 - 0 10214.940 + 0.107 WAG+G4 -4962.011 10076.022 - 1.62e-10 21780.022 - 0 10255.132 - 2.01e-10 WAG+I+G4 -4960.353 10074.706 - 3.13e-10 22086.706 - 0 10256.173 - 1.19e-10 VT+G4 -4964.902 10081.804 - 8.99e-12 21785.804 - 0 10260.914 - 1.12e-11 VT+I+G4 -4962.890 10079.780 - 2.47e-11 22091.780 - 0 10261.247 - 9.45e-12 LG+F+G4 -4936.023 10062.047 - 1.75e-07 28302.047 - 0 10285.934 - 4.12e-17 LG+F+I+G4 -4935.911 10063.822 - 7.22e-08 28687.822 - 0 10290.066 - 5.22e-18 JTT+I+G4 -4981.805 10117.610 - 1.51e-19 22129.610 - 0 10299.076 - 5.76e-20 JTT+G4 -4984.371 10120.741 - 3.15e-20 21824.741 - 0 10299.851 - 3.91e-20 WAG+F+G4 -4954.595 10099.190 - 1.51e-15 28339.190 - 0 10323.078 - 3.54e-25 WAG+F+I+G4 -4953.202 10098.405 - 2.23e-15 28722.405 - 0 10324.649 - 1.61e-25 VT+F+G4 -4966.740 10123.481 - 8.01e-21 28363.481 - 0 10347.368 - 1.88e-30 VT+F+I+G4 -4964.816 10121.631 - 2.02e-20 28745.631 - 0 10347.875 - 1.46e-30 JTT+F+I+G4 -4971.389 10134.778 - 2.82e-23 28758.778 - 0 10361.022 - 2.04e-33 JTT+F+G4 -4973.765 10137.529 - 7.13e-24 28377.529 - 0 10361.416 - 1.67e-33 WAG+I -5022.312 10196.623 - 1.05e-36 21900.623 - 0 10375.733 - 1.3e-36 VT+I -5027.047 10206.094 - 9.21e-39 21910.094 - 0 10385.204 - 1.14e-38 WAG -5031.840 10213.681 - 2.08e-40 15913.681 + 0.996 10390.434 - 8.37e-40 VT -5037.322 10224.644 - 8.64e-43 15924.644 - 0.00414 10401.397 - 3.48e-42 LG+I -5035.178 10222.356 - 2.71e-42 21926.356 - 0 10401.465 - 3.37e-42 LG -5041.431 10232.863 - 1.42e-44 15932.863 - 6.8e-05 10409.616 - 5.72e-44 WAG+F+I -5016.272 10222.545 - 2.47e-42 28462.545 - 0 10446.432 - 5.79e-52 WAG+F -5024.354 10236.708 - 2.07e-45 28096.708 - 0 10458.238 - 1.58e-54 JTT+I -5063.737 10279.473 - 1.07e-54 21983.473 - 0 10458.583 - 1.33e-54 VT+F+I -5025.275 10240.551 - 3.04e-46 28480.551 - 0 10464.438 - 7.13e-56 LG+F+I -5026.912 10243.823 - 5.91e-47 28483.823 - 0 10467.711 - 1.39e-56 LG+F -5032.244 10252.488 - 7.77e-49 28112.488 - 0 10474.018 - 5.92e-58 VT+F -5034.361 10256.722 - 9.35e-50 28116.722 - 0 10478.253 - 7.13e-59 JTT -5078.014 10306.028 - 1.84e-60 16006.028 - 8.81e-21 10482.782 - 7.41e-60 JTT+F+I -5044.421 10278.841 - 1.47e-54 28518.841 - 0 10502.729 - 3.45e-64 JTT+F -5056.094 10300.188 - 3.41e-59 28160.188 - 0 10521.718 - 2.6e-68 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: 1.4868 Category Relative_rate Proportion 1 0.2233 0.2500 2 0.5863 0.2500 3 1.0496 0.2500 4 2.1407 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: -4929.8512 (s.e. 173.2473) Unconstrained log-likelihood (without tree): -339.8233 Number of free parameters (#branches + #model parameters): 76 Akaike information criterion (AIC) score: 10011.7025 Corrected Akaike information criterion (AICc) score: 21715.7025 Bayesian information criterion (BIC) score: 10190.8123 Total tree length (sum of branch lengths): 33.3793 Sum of internal branch lengths: 16.6555 (49.8978% of tree length) WARNING: 1 near-zero internal branches (<0.0128) 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 | +--| (28/64) | | +--Q9ULD4_PWWP1 | +--------------| (99.7/100) | | +--P55201_PWWP1 | +--| (77.3/60) | | | +--Q9Y6K1_PWWP1 | | | +----| (91.7/69) | | | | | +**Q9UBC3_PWWP1 | | | | +---| (97.6/100) | | | | +--O88509_PWWP1 | | | +-----| (64.1/62) | | | | | +---Q96N64_PWWP1 | | | | +---------| (96.3/99) | | | | +--Q6NUJ5_PWWP1 | | | +---| (82.3/50) | | | | +------------Q9P267_PWWP1 | | | +--| (24.7/15) | | | | | +-------Q49A26_PWWP1 | | | | | +--| (75.6/65) | | | | | | | +**P51858_PWWP1 | | | | | | | +**| (0/100) | | | | | | | | +**Q8VHK7_PWWP1 | | | | | | | +--------| (99.3/97) | | | | | | | | | +--Q5TGJ6_PWWP1 | | | | | | | | +--| (82.9/82) | | | | | | | | | +--Q7Z4V5_PWWP1 | | | | | | | | | +--| (91.9/96) | | | | | | | | | | +--O75475_PWWP1 | | | | | | | | +--| (92.1/97) | | | | | | | | | +**Q9Y3E1_PWWP1 | | | | | | | | +--| (74.4/98) | | | | | | | | +**Q9JMG7_PWWP1 | | | | | | +---| (92.9/93) | | | | | | +--Q9VAA9_PWWP1 | | | | +--| (0/16) | | | | | +--Q96L73_PWWP2 | | | | | +--| (86.7/95) | | | | | | +--O96028_PWWP2 | | | | +------------------| (99.8/100) | | | | +--Q9BZ95_PWWP2 | | | +--| (77/41) | | | | | +**Q15326_PWWP1 | | | | | +----| (89.1/99) | | | | | | +--Q8R5C8_PWWP1 | | | | +-----------| (99.5/100) | | | | +-------Q9ULU4_PWWP1 | | | +--| (72.1/30) | | | | | +---Q2TAK8_PWWP1 | | | | | +--| (67.9/83) | | | | | | +--Q5H9M0_PWWP1 | | | | | +----------------------| (100/100) | | | | | | +--A0A494C071_PWWP1 | | | | +--| (71.7/34) | | | | | +----------Q9H0M4_PWWP1 | | | | | +--| (44.1/32) | | | | | | +-------------------Q586Y0_PWWP1 | | | | +--| (73.6/32) | | | | +-------------------Q504Y3_PWWP1 | | +--| (86.4/71) | | | +--------P52701_PWWP1 | | +--| (77.7/52) | | | +-------Q96L73_PWWP1 | | | +--| (75.3/71) | | | | +--O96028_PWWP1 | | +------| (97.1/99) | | +--Q9BZ95_PWWP1 +-------------------| (99.8/100) | +------------O59676_PWWP1 | +----| (87.9/92) | | +-------O94312_PWWP1 +--| (72.9/72) +---------Q04213_PWWP1 Tree in newick format: (P29374_PWWP1:1.0635223602,Q4LE39_PWWP1:0.0140052014,((((O95696_PWWP1:0.2264658398,Q9ULD4_PWWP1:0.1388776833)28/64:0.0391966965,P55201_PWWP1:0.2068983906)99.7/100:1.4003885110,(((((((Q9Y6K1_PWWP1:0.2486136850,(Q9UBC3_PWWP1:0.0000025823,O88509_PWWP1:0.0346957180)97.6/100:0.4268002584)91.7/69:0.5123901198,(Q96N64_PWWP1:0.3853992098,Q6NUJ5_PWWP1:0.0617308128)96.3/99:0.9033280004)64.1/62:0.5346738500,Q9P267_PWWP1:1.2146930238)82.3/50:0.3906822151,((Q49A26_PWWP1:0.7784958054,(((P51858_PWWP1:0.0000010000,Q8VHK7_PWWP1:0.0000010000)0/100:0.0000022991,(Q5TGJ6_PWWP1:0.2586620956,((Q7Z4V5_PWWP1:0.1304455355,O75475_PWWP1:0.1612071778)91.9/96:0.0981943195,(Q9Y3E1_PWWP1:0.0000010000,Q9JMG7_PWWP1:0.0000010000)74.4/98:0.0192236365)92.1/97:0.1325531540)82.9/82:0.0442354467)99.3/97:0.8309548879,Q9VAA9_PWWP1:0.2669051033)92.9/93:0.4360820842)75.6/65:0.2625303924,((Q96L73_PWWP2:0.1545860858,O96028_PWWP2:0.1875321951)86.7/95:0.1602084862,Q9BZ95_PWWP2:0.0152173772)99.8/100:1.7157268270)0/16:0.0471681552)24.7/15:0.1235380074,((Q15326_PWWP1:0.0000028522,Q8R5C8_PWWP1:0.0135763277)89.1/99:0.4678908745,Q9ULU4_PWWP1:0.7563368901)99.5/100:1.1059805370)77/41:0.1482980958,(((Q2TAK8_PWWP1:0.3658932928,Q5H9M0_PWWP1:0.1399639110)67.9/83:0.1466262746,A0A494C071_PWWP1:0.3435006546)100/100:2.0452561750,((Q9H0M4_PWWP1:0.9744708409,Q586Y0_PWWP1:1.7568776336)44.1/32:0.1243735060,Q504Y3_PWWP1:1.8185080526)73.6/32:0.1764445632)71.7/34:0.1959264517)72.1/30:0.1269719470,(P52701_PWWP1:0.8091295885,((Q96L73_PWWP1:0.7699145845,O96028_PWWP1:0.1760001724)75.3/71:0.1567025951,Q9BZ95_PWWP1:0.3507408622)97.1/99:0.6252460866)77.7/52:0.1708604459)86.4/71:0.3144622501)77.3/60:0.2302031452,((O59676_PWWP1:1.2012976942,O94312_PWWP1:0.7558833699)87.9/92:0.4439253286,Q04213_PWWP1:0.9244668427)72.9/72:0.2807254496)99.8/100:1.8369594180); CONSENSUS TREE -------------- Consensus tree is constructed from 1000 bootstrap trees Log-likelihood of consensus tree: -4930.161562 Robinson-Foulds distance between ML tree and consensus tree: 6 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 | +--| (64) | | +--Q9ULD4_PWWP1 | +--------------| (100) | | +--P55201_PWWP1 | +--| (60) | | | +--Q9Y6K1_PWWP1 | | | +----| (69) | | | | | +--Q9UBC3_PWWP1 | | | | +---| (100) | | | | +--O88509_PWWP1 | | | +-----| (62) | | | | | +---Q96N64_PWWP1 | | | | +---------| (99) | | | | +--Q6NUJ5_PWWP1 | | | +---| (50) | | | | +------------Q9P267_PWWP1 | | | +--| (41) | | | | | +--------Q49A26_PWWP1 | | | | | +--| (65) | | | | | | | +--P51858_PWWP1 | | | | | | | +--| (100) | | | | | | | | +--Q8VHK7_PWWP1 | | | | | | | +--------| (97) | | | | | | | | | +--Q5TGJ6_PWWP1 | | | | | | | | +--| (82) | | | | | | | | | +--Q7Z4V5_PWWP1 | | | | | | | | | +--| (96) | | | | | | | | | | +--O75475_PWWP1 | | | | | | | | +--| (97) | | | | | | | | | +--Q9Y3E1_PWWP1 | | | | | | | | +--| (98) | | | | | | | | +--Q9JMG7_PWWP1 | | | | | | +---| (93) | | | | | | +--Q9VAA9_PWWP1 | | | | | +--| (34) | | | | | | | +--Q15326_PWWP1 | | | | | | | +---| (99) | | | | | | | | +--Q8R5C8_PWWP1 | | | | | | +------------| (100) | | | | | | +--------Q9ULU4_PWWP1 | | | | +--| (18) | | | | | +--Q96L73_PWWP2 | | | | | +--| (95) | | | | | | +--O96028_PWWP2 | | | | +-------------------| (100) | | | | +--Q9BZ95_PWWP2 | | | +--| (30) | | | | | +---Q2TAK8_PWWP1 | | | | | +--| (83) | | | | | | +--Q5H9M0_PWWP1 | | | | | +----------------------| (100) | | | | | | +--A0A494C071_PWWP1 | | | | +--| (34) | | | | | +-----------Q9H0M4_PWWP1 | | | | | +--| (34) | | | | | | +-------------------Q504Y3_PWWP1 | | | | +--| (32) | | | | +--------------------Q586Y0_PWWP1 | | +--| (71) | | | +--------P52701_PWWP1 | | +--| (52) | | | +-------Q96L73_PWWP1 | | | +--| (71) | | | | +--O96028_PWWP1 | | +------| (99) | | +---Q9BZ95_PWWP1 +-------------------| (100) | +------------O59676_PWWP1 | +----| (92) | | +-------O94312_PWWP1 +--| (72) +---------Q04213_PWWP1 Consensus tree in newick format: (P29374_PWWP1:1.0681243474,Q4LE39_PWWP1:0.0106643142,((((O95696_PWWP1:0.2275044141,Q9ULD4_PWWP1:0.1397958743)64:0.0380053066,P55201_PWWP1:0.2085513749)100:1.3695726764,((((((Q9Y6K1_PWWP1:0.2521488227,(Q9UBC3_PWWP1:0.0000025829,O88509_PWWP1:0.0346853936)100:0.4236734141)69:0.4976881840,(Q96N64_PWWP1:0.3851120498,Q6NUJ5_PWWP1:0.0621909378)99:0.9187079509)62:0.5279541651,Q9P267_PWWP1:1.1898334304)50:0.4034570813,(((Q49A26_PWWP1:0.7966211050,(((P51858_PWWP1:0.0000025829,Q8VHK7_PWWP1:0.0000025829)100:0.0000026862,(Q5TGJ6_PWWP1:0.2587817357,((Q7Z4V5_PWWP1:0.1308140231,O75475_PWWP1:0.1614966630)96:0.0980648779,(Q9Y3E1_PWWP1:0.0000025829,Q9JMG7_PWWP1:0.0000025829)98:0.0192597333)97:0.1327691806)82:0.0440541991)97:0.8309184824,Q9VAA9_PWWP1:0.2638633025)93:0.4288048542)65:0.2095008122,((Q15326_PWWP1:0.0000025924,Q8R5C8_PWWP1:0.0135830416)99:0.4182699245,Q9ULU4_PWWP1:0.8123071522)100:1.1393839360)34:0.1456163027,((Q96L73_PWWP2:0.1547506519,O96028_PWWP2:0.1876535742)95:0.1614921239,Q9BZ95_PWWP2:0.0144465706)100:1.7624266538)18:0.0029986163)41:0.2317271211,(((Q2TAK8_PWWP1:0.3668537274,Q5H9M0_PWWP1:0.1408097928)83:0.1454356368,A0A494C071_PWWP1:0.3458441606)100:2.0673062856,((Q9H0M4_PWWP1:1.1090791453,Q504Y3_PWWP1:1.7980800271)34:0.0000022777,Q586Y0_PWWP1:1.8331959639)32:0.2391320453)34:0.1752029318)30:0.0903185285,(P52701_PWWP1:0.8301605655,((Q96L73_PWWP1:0.7708770595,O96028_PWWP1:0.1788960945)71:0.1456755248,Q9BZ95_PWWP1:0.3592994543)99:0.6176735649)52:0.1735898121)71:0.3157350764)60:0.2297351150,((O59676_PWWP1:1.1988196795,O94312_PWWP1:0.7576630246)92:0.4637884294,Q04213_PWWP1:0.8946923736)72:0.2748444697)100:1.8149789535); 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/primary.treefile -m "LG+G4{1.48681}" --length 78 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_masked.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_masked.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 12:59:53 2026 Total CPU time used: 581.393153 seconds (0h:9m:41s) Total wall-clock time used: 316.8141536 seconds (0h:5m:16s)