IQ-TREE 3.0.1 built Jul 9 2025 Input file name: input Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (1000 replicates) Random seed number: 352531 REFERENCES ---------- To cite IQ-TREE 3 please use: Thomas K.F. Wong, Nhan Ly-Trong, Huaiyan Ren, Hector Banos, Andrew J. Roger, Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W. Hahn, Gavin Huttley, Robert Lanfear, Bui Quang Minh (2025) IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. Submitted. Please also cite the following paper(s) for the feature(s) that you used: 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: 18 sequences with 29670 amino-acid sites Number of constant sites: 8837 (= 29.7843% of all sites) Number of invariant (constant or ambiguous constant) sites: 8837 (= 29.7843% of all sites) Number of parsimony informative sites: 18194 Number of distinct site patterns: 21041 ModelFinder ----------- Best-fit model according to BIC: LG+F+R5 List of models sorted by BIC scores: Model LogL AIC w-AIC AICc w-AICc BIC w-BIC LG+F+R5 -428731.468 857582.936 + 1 857583.183 + 1 858080.809 + 0.999 LG+F+I+R3 -428754.290 857622.579 - 2.46e-09 857622.802 - 2.49e-09 858095.559 - 0.000626 Q.PFAM+F+R5 -428863.018 857846.036 - 7.39e-58 857846.283 - 7.39e-58 858343.910 - 7.38e-58 Q.PFAM+F+I+R3 -428890.903 857895.806 - 1.15e-68 857896.029 - 1.17e-68 858368.786 - 2.93e-63 Q.YEAST+F+R5 -429136.938 858393.875 - 8.07e-177 858394.123 - 8.07e-177 858891.749 - 8.06e-177 Q.YEAST+F+I+R3 -429181.836 858477.673 - 5.13e-195 858477.896 - 5.19e-195 858950.653 - 1.31e-189 RTREV+F+R5 -429612.145 859344.291 - 0 859344.538 - 0 859842.164 - 0 RTREV+F+I+R3 -429651.957 859417.914 - 0 859418.137 - 0 859890.894 - 0 Q.PFAM+R5 -429851.067 859784.135 - 0 859784.251 - 0 860124.348 - 0 Q.PFAM+I+R3 -429875.050 859826.100 - 0 859826.200 - 0 860141.420 - 0 WAG+F+R5 -429931.206 859982.412 - 0 859982.660 - 0 860480.286 - 0 WAG+F+I+R3 -429950.510 860015.020 - 0 860015.243 - 0 860488.000 - 0 LG+R5 -430136.353 860354.706 - 0 860354.822 - 0 860694.919 - 0 LG+I+R3 -430153.348 860382.695 - 0 860382.795 - 0 860698.015 - 0 LG+R4 -430153.128 860384.256 - 0 860384.361 - 0 860707.874 - 0 LG+R6 -430134.096 860354.192 - 0 860354.320 - 0 860711.002 - 0 LG+I+R4 -430153.000 860385.999 - 0 860386.110 - 0 860717.915 - 0 LG+I+G4 -430198.575 860467.151 - 0 860467.236 - 0 860757.577 - 0 LG+R3 -430328.234 860730.467 - 0 860730.562 - 0 861037.489 - 0 LG+G4 -430397.931 860863.863 - 0 860863.943 - 0 861145.991 - 0 LG+I+R2 -430490.010 861052.021 - 0 861052.110 - 0 861350.745 - 0 Q.INSECT+F+R5 -430431.317 860982.634 - 0 860982.881 - 0 861480.507 - 0 Q.INSECT+F+I+R3 -430470.322 861054.644 - 0 861054.867 - 0 861527.624 - 0 WAG+R5 -430643.072 861368.144 - 0 861368.260 - 0 861708.358 - 0 WAG+I+R3 -430661.364 861398.728 - 0 861398.828 - 0 861714.048 - 0 VT+F+R5 -430724.591 861569.183 - 0 861569.430 - 0 862067.056 - 0 VT+F+I+R3 -430743.962 861601.924 - 0 861602.147 - 0 862074.903 - 0 Q.YEAST+R5 -431297.442 862676.885 - 0 862677.001 - 0 863017.098 - 0 Q.YEAST+I+R3 -431338.302 862752.605 - 0 862752.705 - 0 863067.924 - 0 LG+R2 -431788.267 863646.534 - 0 863646.619 - 0 863936.960 - 0 VT+R5 -431799.902 863681.804 - 0 863681.920 - 0 864022.017 - 0 VT+I+R3 -431817.939 863711.878 - 0 863711.978 - 0 864027.198 - 0 BLOSUM62+F+R5 -431768.201 863656.403 - 0 863656.650 - 0 864154.276 - 0 BLOSUM62+F+I+R3 -431787.322 863688.644 - 0 863688.867 - 0 864161.624 - 0 Q.INSECT+R5 -431926.031 863934.061 - 0 863934.178 - 0 864274.275 - 0 Q.INSECT+I+R3 -431961.757 863999.513 - 0 863999.613 - 0 864314.833 - 0 PMB+F+R5 -432322.845 864765.689 - 0 864765.937 - 0 865263.563 - 0 PMB+F+I+R3 -432343.020 864800.041 - 0 864800.264 - 0 865273.020 - 0 CPREV+F+R5 -432665.710 865451.420 - 0 865451.667 - 0 865949.293 - 0 CPREV+F+I+R3 -432718.978 865551.956 - 0 865552.179 - 0 866024.936 - 0 DAYHOFF+F+R5 -433104.552 866329.103 - 0 866329.351 - 0 866826.977 - 0 DCMUT+F+R5 -433111.330 866342.660 - 0 866342.907 - 0 866840.534 - 0 DAYHOFF+F+I+R3 -433158.228 866430.456 - 0 866430.680 - 0 866903.436 - 0 DCMUT+F+I+R3 -433166.049 866446.099 - 0 866446.322 - 0 866919.078 - 0 JTTDCMUT+F+R5 -433323.596 866767.192 - 0 866767.440 - 0 867265.066 - 0 JTTDCMUT+F+I+R3 -433363.434 866840.868 - 0 866841.091 - 0 867313.848 - 0 JTT+F+R5 -433423.717 866967.434 - 0 866967.681 - 0 867465.307 - 0 JTT+F+I+R3 -433450.521 867015.043 - 0 867015.266 - 0 867488.023 - 0 BLOSUM62+I+R3 -433636.472 867348.943 - 0 867349.043 - 0 867664.263 - 0 BLOSUM62+R5 -433621.551 867325.102 - 0 867325.218 - 0 867665.315 - 0 PMB+R5 -434162.111 868406.222 - 0 868406.338 - 0 868746.436 - 0 PMB+I+R3 -434178.221 868432.441 - 0 868432.541 - 0 868747.761 - 0 JTTDCMUT+R5 -434345.181 868772.362 - 0 868772.478 - 0 869112.575 - 0 JTTDCMUT+I+R3 -434381.873 868839.746 - 0 868839.846 - 0 869155.066 - 0 JTT+R5 -434455.633 868993.266 - 0 868993.382 - 0 869333.479 - 0 JTT+I+R3 -434479.414 869034.827 - 0 869034.927 - 0 869350.147 - 0 RTREV+R5 -434699.089 869480.179 - 0 869480.295 - 0 869820.392 - 0 RTREV+I+R3 -434735.959 869547.919 - 0 869548.019 - 0 869863.239 - 0 DAYHOFF+R5 -434802.932 869687.863 - 0 869687.979 - 0 870028.077 - 0 DCMUT+R5 -434814.596 869711.192 - 0 869711.308 - 0 870051.406 - 0 DAYHOFF+I+R3 -434853.138 869782.276 - 0 869782.376 - 0 870097.596 - 0 DCMUT+I+R3 -434865.856 869807.712 - 0 869807.812 - 0 870123.032 - 0 MTINV+F+R5 -435130.915 870381.831 - 0 870382.078 - 0 870879.704 - 0 MTINV+F+I+R3 -435207.557 870529.113 - 0 870529.337 - 0 871002.093 - 0 Q.PLANT+F+R5 -435571.811 871263.622 - 0 871263.870 - 0 871761.496 - 0 CPREV+R5 -435686.408 871454.815 - 0 871454.931 - 0 871795.029 - 0 CPREV+I+R3 -435729.762 871535.525 - 0 871535.625 - 0 871850.845 - 0 Q.PLANT+F+I+R3 -435647.712 871409.424 - 0 871409.648 - 0 871882.404 - 0 Q.PLANT+R5 -436058.822 872199.643 - 0 872199.759 - 0 872539.857 - 0 Q.PLANT+I+R3 -436128.992 872333.985 - 0 872334.085 - 0 872649.304 - 0 LG+I -436383.590 872835.181 - 0 872835.261 - 0 873117.309 - 0 MTZOA+F+R5 -436266.717 872653.434 - 0 872653.681 - 0 873151.308 - 0 MTZOA+F+I+R3 -436402.273 872918.545 - 0 872918.769 - 0 873391.525 - 0 MTMET+F+R5 -438472.719 877065.438 - 0 877065.685 - 0 877563.311 - 0 MTMET+F+I+R3 -438588.146 877290.292 - 0 877290.516 - 0 877763.272 - 0 MTREV+F+R5 -438974.855 878069.709 - 0 878069.956 - 0 878567.583 - 0 MTREV+F+I+R3 -439075.164 878264.328 - 0 878264.551 - 0 878737.308 - 0 FLU+F+R5 -439190.241 878500.482 - 0 878500.729 - 0 878998.356 - 0 Q.MAMMAL+F+R5 -439214.353 878548.707 - 0 878548.954 - 0 879046.580 - 0 FLU+F+I+R3 -439294.840 878703.680 - 0 878703.903 - 0 879176.660 - 0 Q.MAMMAL+F+I+R3 -439294.930 878703.859 - 0 878704.082 - 0 879176.839 - 0 Q.MAMMAL+R5 -439914.827 879911.653 - 0 879911.770 - 0 880251.867 - 0 Q.MAMMAL+I+R3 -439991.993 880059.987 - 0 880060.087 - 0 880375.307 - 0 MTART+F+R5 -440411.717 880943.435 - 0 880943.682 - 0 881441.308 - 0 MTART+F+I+R3 -440623.772 881361.544 - 0 881361.767 - 0 881834.524 - 0 HIVB+F+R5 -442302.858 884725.715 - 0 884725.962 - 0 885223.589 - 0 HIVB+F+I+R3 -442418.681 884951.361 - 0 884951.585 - 0 885424.341 - 0 Q.BIRD+F+R5 -442723.958 885567.915 - 0 885568.162 - 0 886065.789 - 0 Q.BIRD+F+I+R3 -442836.300 885786.600 - 0 885786.824 - 0 886259.580 - 0 FLU+R5 -443248.201 886578.403 - 0 886578.519 - 0 886918.616 - 0 FLU+I+R3 -443351.708 886779.416 - 0 886779.516 - 0 887094.736 - 0 Q.BIRD+R5 -443339.390 886760.779 - 0 886760.896 - 0 887100.993 - 0 Q.BIRD+I+R3 -443431.293 886938.586 - 0 886938.686 - 0 887253.906 - 0 MTVER+F+R5 -444782.985 889685.970 - 0 889686.217 - 0 890183.844 - 0 MTVER+F+I+R3 -444960.998 890035.997 - 0 890036.220 - 0 890508.977 - 0 HIVB+R5 -446796.881 893675.761 - 0 893675.878 - 0 894015.975 - 0 HIVB+I+R3 -446887.370 893850.739 - 0 893850.839 - 0 894166.059 - 0 MTMAM+F+R5 -448701.384 897522.768 - 0 897523.015 - 0 898020.642 - 0 LG -448883.275 897832.549 - 0 897832.625 - 0 898106.380 - 0 MTMAM+F+I+R3 -448952.615 898019.229 - 0 898019.453 - 0 898492.209 - 0 FLAVI+F+R5 -449914.053 899948.106 - 0 899948.354 - 0 900445.980 - 0 FLAVI+F+I+R3 -450075.133 900264.266 - 0 900264.490 - 0 900737.246 - 0 MTZOA+R5 -451765.657 903613.314 - 0 903613.431 - 0 903953.528 - 0 MTZOA+I+R3 -451863.642 903803.284 - 0 903803.384 - 0 904118.603 - 0 FLAVI+R5 -453304.588 906691.176 - 0 906691.292 - 0 907031.390 - 0 FLAVI+I+R3 -453477.673 907031.347 - 0 907031.447 - 0 907346.666 - 0 HIVW+F+R5 -454002.686 908125.372 - 0 908125.619 - 0 908623.245 - 0 HIVW+F+I+R3 -454102.889 908319.778 - 0 908320.001 - 0 908792.758 - 0 MTMET+R5 -459624.315 919330.631 - 0 919330.747 - 0 919670.844 - 0 MTMET+I+R3 -459675.847 919427.693 - 0 919427.793 - 0 919743.013 - 0 MTINV+R5 -460612.305 921306.611 - 0 921306.727 - 0 921646.824 - 0 MTINV+I+R3 -460637.219 921350.439 - 0 921350.539 - 0 921665.759 - 0 MTART+R5 -460633.617 921349.235 - 0 921349.351 - 0 921689.449 - 0 MTREV+R5 -460749.256 921580.513 - 0 921580.629 - 0 921920.726 - 0 MTART+I+R3 -460824.389 921724.778 - 0 921724.878 - 0 922040.098 - 0 MTREV+I+R3 -460824.511 921725.022 - 0 921725.122 - 0 922040.341 - 0 HIVW+R5 -464630.357 929342.713 - 0 929342.830 - 0 929682.927 - 0 HIVW+I+R3 -464733.537 929543.075 - 0 929543.175 - 0 929858.394 - 0 MTVER+R5 -465485.542 931053.084 - 0 931053.201 - 0 931393.298 - 0 MTVER+I+R3 -465586.576 931249.152 - 0 931249.252 - 0 931564.471 - 0 MTMAM+R5 -471053.162 942188.324 - 0 942188.440 - 0 942528.538 - 0 MTMAM+I+R3 -471328.495 942732.991 - 0 942733.091 - 0 943048.311 - 0 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+F+R5 State frequencies: (empirical counts from alignment) pi(A) = 0.0820 pi(R) = 0.0537 pi(N) = 0.0351 pi(D) = 0.0590 pi(C) = 0.0179 pi(Q) = 0.0312 pi(E) = 0.0724 pi(G) = 0.0745 pi(H) = 0.0198 pi(I) = 0.0490 pi(L) = 0.0899 pi(K) = 0.0686 pi(M) = 0.0271 pi(F) = 0.0365 pi(P) = 0.0424 pi(S) = 0.0765 pi(T) = 0.0543 pi(W) = 0.0115 pi(Y) = 0.0281 pi(V) = 0.0705 Model of rate heterogeneity: FreeRate with 5 categories Site proportion and rates: (0.2838,0.0381) (0.2776,0.4516) (0.2694,1.1834) (0.1610,2.8399) (0.0083,10.5613) Category Relative_rate Proportion 1 0.0381 0.2838 2 0.4516 0.2776 3 1.1834 0.2694 4 2.8399 0.1610 5 10.5613 0.0083 MAXIMUM LIKELIHOOD TREE ----------------------- Log-likelihood of the tree: -428712.8075 (s.e. 1580.6923) Unconstrained log-likelihood (without tree): -269599.6953 Number of free parameters (#branches + #model parameters): 60 Akaike information criterion (AIC) score: 857545.6150 Corrected Akaike information criterion (AICc) score: 857545.8622 Bayesian information criterion (BIC) score: 858043.4885 Total tree length (sum of branch lengths): 4.5663 Sum of internal branch lengths: 2.7462 (60.1398% of tree length) NOTE: Tree is UNROOTED although outgroup taxon 'Fragilariopsis_cylindrus' is drawn at root Numbers in parentheses are SH-aLRT support (%) / ultrafast bootstrap support (%) +--Triparma_laevis_f.inornata +--| (100/100) | +--NIES_2565 +----| (100/100) | +**Triparma_laevis_f.longispina +---------| (100/100) | | +--Triparma_verrucosa | | +--| (100/100) | | | +--Triparma_strigata | +----| (100/100) | +--RCC1657 +-----| (100/100) | | +--RCC208 | +-----------------| (100/100) | +--RCC2347 +----| (100/100) | | +---Triparma_retinervis | | +---| (100/100) | | | +--Triparma_columacea | | +---------| (100/100) | | | +-----CCMP1866 | +-----| (100/100) | +--------------------TARA_PON_109_MAG_00217 +--------| (100/100) | +--------------------------Tetraparma_gracilis +----------------| (100/100) | | +--Parmales_sp._scaly_parma | +--------------------------------| (100/100) | +--TARA_ARC_108_MAG_00221 | (100/100) +-------------------Thalassiosira_pseudonana | | +-------Fragilariopsis_cylindrus +-------------------| +------Pseudo-nitzschia_multistriata Tree in newick format: ((Fragilariopsis_cylindrus:0.1486220967,Pseudo-nitzschia_multistriata:0.1284739114):0.3691477509,(((((((Triparma_laevis_f.inornata:0.0070999277,NIES_2565:0.0012960916)100/100:0.0013606199,Triparma_laevis_f.longispina:0.0000020554)100/100:0.0919573776,((Triparma_verrucosa:0.0026482668,Triparma_strigata:0.0018367059)100/100:0.0038435623,RCC1657:0.0066878736)100/100:0.0902748705)100/100:0.1832940119,(RCC208:0.0011708558,RCC2347:0.0019431850)100/100:0.3285020688)100/100:0.1213752506,(((Triparma_retinervis:0.0776760947,Triparma_columacea:0.0661895477)100/100:0.0759472413,CCMP1866:0.1226056390)100/100:0.1942386104,TARA_PON_109_MAG_00217:0.3847831223)100/100:0.1131623444)100/100:0.1012027609,Tetraparma_gracilis:0.4939418484)100/100:0.1705067820,(Parmales_sp._scaly_parma:0.0005476350,TARA_ARC_108_MAG_00221:0.0010114331)100/100:0.5933951690)100/100:0.3079436583,Thalassiosira_pseudonana:0.3735935065)100/100; CONSENSUS TREE -------------- Consensus tree is constructed from 1000 bootstrap trees Log-likelihood of consensus tree: -428712.810567 Robinson-Foulds distance between ML tree and consensus tree: 0 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 (%) +-----Fragilariopsis_cylindrus | (100) | +--Triparma_laevis_f.inornata | +--| (100) | | +--NIES_2565 | +--| (100) | | +--Triparma_laevis_f.longispina | +------| (100) | | | +--Triparma_verrucosa | | | +--| (100) | | | | +--Triparma_strigata | | +--| (100) | | +--RCC1657 | +----| (100) | | | +--RCC208 | | +------------| (100) | | +--RCC2347 | +---| | | | +--Triparma_retinervis | | | +--| (100) | | | | +--Triparma_columacea | | | +-------| (100) | | | | +----CCMP1866 | | +---| (100) | | +--------------TARA_PON_109_MAG_00217 | +------| (100) | | +-------------------Tetraparma_gracilis | +-----------| (100) | | | +--Parmales_sp._scaly_parma | | +-----------------------| (100) | | +--TARA_ARC_108_MAG_00221 +--------------| (100) | +--------------Thalassiosira_pseudonana | +----Pseudo-nitzschia_multistriata Consensus tree in newick format: (Fragilariopsis_cylindrus:0.1486024361,((((((((Triparma_laevis_f.inornata:0.0071035032,NIES_2565:0.0012981929)100:0.0013605986,Triparma_laevis_f.longispina:0.0000026147)100:0.0919880922,((Triparma_verrucosa:0.0026501124,Triparma_strigata:0.0018390142)100:0.0038457435,RCC1657:0.0066900962)100:0.0903155748)100:0.1833569350,(RCC208:0.0011728568,RCC2347:0.0019431915)100:0.3286502414)100:0.1214156664,(((Triparma_retinervis:0.0776979278,Triparma_columacea:0.0662146408)100:0.0759757695,CCMP1866:0.1226387150)100:0.1943163349,TARA_PON_109_MAG_00217:0.3849351874)100:0.1131928058):0.1012053193,Tetraparma_gracilis:0.4941330050)100:0.1705323922,(Parmales_sp._scaly_parma:0.0005473712,TARA_ARC_108_MAG_00221:0.0010133993)100:0.5936070031)100:0.3080235638,Thalassiosira_pseudonana:0.3736872394)100:0.3692440030,Pseudo-nitzschia_multistriata:0.1285359648)100; 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 result/euk_tree.treefile -m "LG+F+R5{0.283752,0.0381225,0.277585,0.451564,0.269379,1.1834,0.160956,2.83992,0.00832753,10.5613}" --length 29670 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 input --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 input --alisim mimicked_MSA --num-alignments 100 For more information on using AliSim, please visit: www.iqtree.org/doc/AliSim TIME STAMP ---------- Date and time: Wed Aug 27 15:40:03 2025 Total CPU time used: 18861.23651 seconds (5h:14m:21s) Total wall-clock time used: 600.4266679 seconds (0h:10m:0s)