IQ-TREE 3.1.3 built Jul 26 2026 Input file name: /home/runner/work/mitophy/mitophy/work/origin/concat.faa Type of analysis: tree reconstruction Random seed number: 42 REFERENCES ---------- To cite IQ-TREE 3 please use: Thomas K.F. Wong, Nhan Ly-Trong, Huaiyan Ren, Piyumal Demotte, Hector Banos, Andrew J. Roger, Edward Susko, Chris Bielow, Nicola De Maio, Nick Goldman, Matthew W. Hahn, Mario dos Reis, Le Sy Vinh, Gavin Huttley, Robert Lanfear, Bui Quang Minh (2026) IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. Molecular Biology and Evolution, msag117. https://doi.org/10.1093/molbev/msag117 SEQUENCE ALIGNMENT ------------------ NOTE: Alignment sequence type is auto-detected. If in doubt, specify it via -st option. Input data: 103 sequences with 10199 amino-acid sites Number of constant sites: 723 (= 7.08893% of all sites) Number of invariant (constant or ambiguous constant) sites: 723 (= 7.08893% of all sites) Number of parsimony informative sites: 8695 Number of distinct site patterns: 9753 SUBSTITUTION PROCESS -------------------- Model of substitution: LG+F+G4 State frequencies: (empirical counts from alignment) pi(A) = 0.0809 pi(R) = 0.0514 pi(N) = 0.0323 pi(D) = 0.0411 pi(C) = 0.0109 pi(Q) = 0.0266 pi(E) = 0.0492 pi(G) = 0.0787 pi(H) = 0.0196 pi(I) = 0.0810 pi(L) = 0.1097 pi(K) = 0.0495 pi(M) = 0.0312 pi(F) = 0.0594 pi(P) = 0.0412 pi(S) = 0.0566 pi(T) = 0.0498 pi(W) = 0.0133 pi(Y) = 0.0351 pi(V) = 0.0826 Model of rate heterogeneity: Gamma with 4 categories Gamma shape alpha: 0.8190 Category Relative_rate Proportion 1 0.0996 0.2500 2 0.4147 0.2500 3 0.9621 0.2500 4 2.5237 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: -821164.8672 (s.e. 5708.3464) Unconstrained log-likelihood (without tree): -93156.7746 Number of free parameters (#branches + #model parameters): 223 Akaike information criterion (AIC) score: 1642775.7344 Corrected Akaike information criterion (AICc) score: 1642785.7499 Bayesian information criterion (BIC) score: 1644388.0345 Total tree length (sum of branch lengths): 47.5069 Sum of internal branch lengths: 13.4424 (28.2957% of tree length) NOTE: Tree is UNROOTED although outgroup taxon 'GCF_000005845.2' is drawn at root Numbers in parentheses are SH-aLRT support (%) +--GCF_000005845.2 | | +--GCF_000006765.1 +--| (100) | | +--GCF_000007125.1 | | +--| (100) | | | +--GCF_019930925.1 | | +--| (45.3) | | | +--GCF_012913625.1 | | +--| (100) | | | | +--GCF_000092025.1 | | | | +--| (100) | | | | | +--GCF_000092045.1 | | | +--| (100) | | | +--GCF_037023865.1 | | +--| (100) | | | | +--GCF_000083545.1 | | | +--| (100) | | | | +--GCF_001642675.1 | | | +--| (100) | | | +--GCF_016584445.1 | | +--| (100) | | | +--GCF_000143145.1 | | +--| (100) | | | | +--GCF_000011965.2 | | | | +--| (100) | | | | | +--GCF_002983865.1 | | | | +--| (100) | | | | | +--GCF_000018145.1 | | | | +--| (100) | | | | | | +--GCF_003324715.1 | | | | | +--| (40.9) | | | | | +--GCF_004063735.1 | | | +--| (98.1) | | | | +--GCF_000013025.1 | | | | +--| (100) | | | | | +--GCF_003634045.1 | | | | +--| (100) | | | | | | +--GCF_000017265.1 | | | | | | +--| (100) | | | | | | | +--GCF_000022005.1 | | | | | +--| (100) | | | | | +--GCF_000144605.1 | | | +--| (100) | | | +--GCF_000152825.2 | | +--| (99.9) | | | | +--GCF_000091125.1 | | | | +--| (100) | | | | | +--GCF_001719165.1 | | | | +--| (100) | | | | | +--GCF_016027095.1 | | | | +--| (73.3) | | | | | +--GCF_017607425.1 | | | | +--| (100) | | | | | +--GCF_000498655.1 | | | +--| (100) | | | | +--GCF_000375545.1 | | | | +--| (100) | | | | | +--GCF_004341375.1 | | | +--| (65.5) | | | +--GCF_006385175.1 | | +--| (100) | | | +--GCF_055385085.1 | | +--| (100) | | | | +--GCF_000013085.1 | | | | +--| (95.9) | | | | | +--GCF_002995515.1 | | | | +--| (100) | | | | | | +--GCF_000583855.1 | | | | | +---| (100) | | | | | +--GCF_009914215.2 | | | | +--| (100) | | | | | | +--GCF_000226315.1 | | | | | | +--| (100) | | | | | | | +--GCF_007827425.1 | | | | | +--| (97) | | | | | | +--GCF_000374005.1 | | | | | +--| (100) | | | | | +--GCF_000515255.1 | | | +--| (99.9) | | | | +--GCF_000427665.1 | | | +--| (100) | | | +--GCF_057418525.1 | | +--| (91.1) | | | | +--GCF_000012345.1 | | | | +--| (100) | | | | | +--GCF_000195085.1 | | | +--| (44) | | | | +--GCF_000012385.1 | | | | +--| (100) | | | | | +--GCF_000277165.1 | | | | +--| (100) | | | | | +----GCF_900327255.1 | | | | +--| (79.2) | | | | | +----GCF_000219355.1 | | | | +--| (100) | | | | | | +--GCF_000013145.1 | | | | | | +--| (100) | | | | | | | +--GCF_000964685.1 | | | | | | +--| (100) | | | | | | | +--GCF_947533255.1 | | | | | +--| (100) | | | | | +------GCF_000013165.1 | | | +--| (98.9) | | | | +---NC_000887.3 | | | | +--| (100) | | | | | +---NC_053320.1 | | | | +--| (100) | | | | | | +--NC_001677.2 | | | | | +--| (100) | | | | | +--NC_002007.1 | | | | +--| (52.9) | | | | | | +----NC_002572.1 | | | | | +--| (100) | | | | | +--NC_010637.1 | | | | +--| (69.2) | | | | | | +-----NC_005332.1 | | | | | | +--| (95.4) | | | | | | | +-----NC_013935.1 | | | | | +--| (86.7) | | | | | +-----NC_017836.1 | | | | +--| (46.1) | | | | | | +---------NC_000946.1 | | | | | | +--| (92.5) | | | | | | | | +---------NC_002573.1 | | | | | | | +--| (88.2) | | | | | | | | +----NC_003029.1 | | | | | | | +----------------------------| (100) | | | | | | | +----NC_058286.1 | | | | | | +--| (70.6) | | | | | | | | +---NC_002174.1 | | | | | | | +--| (100) | | | | | | | +----NC_002571.1 | | | | | | +--| (11.2) | | | | | | | | +------NC_016739.1 | | | | | | | +--| (100) | | | | | | | +-----NC_030223.1 | | | | | | +--| (100) | | | | | | | +-----NC_002387.1 | | | | | +--| (96.6) | | | | | | +----NC_001715.1 | | | | | | +--| (100) | | | | | | | | +----------NC_003053.1 | | | | | | | +--| (78.9) | | | | | | | +-----NC_027264.1 | | | | | +--| (100) | | | | | | +---NC_004309.1 | | | | | +--| (100) | | | | | | +------NC_008151.3 | | | | | +--| (91.1) | | | | | +--------------NC_012920.1 | | | | +--| (58.2) | | | | | | +------------NC_000895.1 | | | | | | +--| (100) | | | | | | | +-------NC_001637.1 | | | | | +--| (11.6) | | | | | +----NC_029886.1 | | | | +--| (99.6) | | | | | +----NC_002553.1 | | | +---| (100) | | | | +--NC_001613.1 | | | | +--| (96) | | | | | +--NC_008239.1 | | | | +--| (71.5) | | | | | | +--NC_005255.1 | | | | | | +--| (100) | | | | | | | | +--NC_007945.1 | | | | | | | +--| (100) | | | | | | | +--NC_037508.1 | | | | | +--| (100) | | | | | +--NC_009630.1 | | | | +--| (100) | | | | | +----NC_008240.1 | | | +--| (34.9) | | | | +--NC_001823.1 | | | | +--| (100) | | | | | +--NC_021125.1 | | | | +--| (35.8) | | | | | +---NC_021128.1 | | | | +--| (100) | | | | | | +----NC_021126.1 | | | | | +--| (70.3) | | | | | +-------NC_021127.1 | | | | +--| (100) | | | | | +----NC_021124.1 | | | +--| (21.3) | | | +----NC_036491.1 | | +--| (100) | | | | +--GCF_000388175.3 | | | +---------| (100) | | | +--GCF_000469665.2 | | +--| (100) | | | +----GCF_000014865.1 | +---| (100) | | +--GCF_001718895.1 | | +--| (100) | | | +--GCF_014142625.1 | | +--| (62.6) | | | +---GCF_022869645.1 | | +--| (100) | | | +--GCF_054182965.1 | +--| (90.4) | +---GCF_013388375.1 | +----GCF_008369605.1 Tree in newick format: (GCF_000005845.2:0.1497361657,(GCF_000006765.1:0.1823325463,(((((((((((((GCF_000007125.1:0.0677310063,GCF_019930925.1:0.2331577674)100:0.0427701877,GCF_012913625.1:0.0976519658)45.3:0.0233969451,((GCF_000092025.1:0.0632658986,GCF_000092045.1:0.0656235855)100:0.0229195683,GCF_037023865.1:0.0448720004)100:0.0677186927)100:0.1031378671,(GCF_000083545.1:0.2062890313,(GCF_001642675.1:0.0710100360,GCF_016584445.1:0.0659536262)100:0.1242946849)100:0.0548017432)100:0.0396098770,GCF_000143145.1:0.2784121374)100:0.0617660447,((((GCF_000011965.2:0.0760234227,GCF_002983865.1:0.0851116342)100:0.0437239471,GCF_000018145.1:0.0911343648)100:0.0359397565,(GCF_003324715.1:0.1071860207,GCF_004063735.1:0.1411496031)40.9:0.0322604095)100:0.2587814747,(((GCF_000013025.1:0.3262945223,GCF_003634045.1:0.2077654597)100:0.0565120137,((GCF_000017265.1:0.1082758984,GCF_000022005.1:0.1217984184)100:0.0505956486,GCF_000144605.1:0.1850623297)100:0.1372378820)100:0.0470951291,GCF_000152825.2:0.3203822425)100:0.0509806536)98.1:0.0344290297)100:0.0648168092,(((((GCF_000091125.1:0.0949566211,GCF_001719165.1:0.2118993606)100:0.0345119542,GCF_016027095.1:0.1168381285)100:0.0343557847,GCF_017607425.1:0.0990378085)73.3:0.0377635311,GCF_000498655.1:0.1645972830)100:0.2320118345,((GCF_000375545.1:0.1848945861,GCF_004341375.1:0.2397280865)100:0.0513660306,GCF_006385175.1:0.2166101807)65.5:0.0333555856)100:0.0454104757)99.9:0.0303663629,GCF_055385085.1:0.2364161045)100:0.0313875521,((((GCF_000013085.1:0.2727109987,GCF_002995515.1:0.1918040671)95.9:0.0488495844,(GCF_000583855.1:0.1457773129,GCF_009914215.2:0.1027988726)100:0.3958805914)100:0.0311353412,((GCF_000226315.1:0.3185192493,GCF_007827425.1:0.1715823354)100:0.0459592904,(GCF_000374005.1:0.2050711828,GCF_000515255.1:0.2258006756)100:0.0626208064)97:0.0220858641)100:0.0303079034,(GCF_000427665.1:0.3137124388,GCF_057418525.1:0.2090564851)100:0.0521246670)99.9:0.0278934547)100:0.0621465113,((GCF_000012345.1:0.2942913553,GCF_000195085.1:0.2468708170)100:0.2591098490,(((((GCF_000012385.1:0.1231184677,GCF_000277165.1:0.0581595097)100:0.2302560632,GCF_900327255.1:0.4662634839)100:0.1611024703,GCF_000219355.1:0.4950302570)79.2:0.0417132364,(((GCF_000013145.1:0.1577617068,GCF_000964685.1:0.3061303496)100:0.1561422397,GCF_947533255.1:0.2834250816)100:0.1703906703,GCF_000013165.1:0.6955997058)100:0.1606743255)100:0.0847533421,((((((((NC_000887.3:0.4459473538,NC_053320.1:0.4027430533)100:0.1981216504,(NC_001677.2:0.2678129387,NC_002007.1:0.3271612400)100:0.1537794112)100:0.1360321647,(NC_002572.1:0.4673058377,NC_010637.1:0.3281333826)100:0.1712352853)52.9:0.0382731109,((NC_005332.1:0.6243489294,NC_013935.1:0.5838317305)95.4:0.0907721141,NC_017836.1:0.5618713250)86.7:0.0464443515)69.2:0.0293079326,(((((NC_000946.1:0.9668747191,(NC_002573.1:0.9733612076,(NC_003029.1:0.4672234019,NC_058286.1:0.5049297638)100:2.6194300726)88.2:0.2250403883)92.5:0.1016160913,(NC_002174.1:0.4376364837,NC_002571.1:0.4858157353)100:0.2490725035)70.6:0.0872124519,(NC_016739.1:0.6493232267,NC_030223.1:0.5440606744)100:0.1186006707)11.2:0.0536155892,NC_002387.1:0.5469991469)100:0.0771508020,((NC_001715.1:0.5200195884,(NC_003053.1:1.0240183426,NC_027264.1:0.6187334714)78.9:0.1356956168)100:0.2395839160,(NC_004309.1:0.4199832510,(NC_008151.3:0.6522431360,NC_012920.1:1.4318821793)91.1:0.0991664190)100:0.1589149219)100:0.1341379140)96.6:0.0407480852)46.1:0.0358489978,((NC_000895.1:1.1808954073,NC_001637.1:0.7528748642)100:0.2036472164,NC_029886.1:0.5236994629)11.6:0.0728238932)58.2:0.0413306450,NC_002553.1:0.4602085824)99.6:0.0414440916,((((NC_001613.1:0.3316815693,NC_008239.1:0.2537989781)96:0.0415778666,((NC_005255.1:0.0743665596,(NC_007945.1:0.0350873529,NC_037508.1:0.0430796884)100:0.0364226384)100:0.1615975652,NC_009630.1:0.1847749368)100:0.0508245519)71.5:0.0402327220,NC_008240.1:0.4731228026)100:0.1247560888,(((((NC_001823.1:0.2121767156,NC_021125.1:0.2532088126)100:0.2091482472,NC_021128.1:0.4122524318)35.8:0.0655502106,(NC_021126.1:0.4581688501,NC_021127.1:0.7260598022)70.3:0.0810903325)100:0.1421882237,NC_021124.1:0.4649208721)100:0.0719921337,NC_036491.1:0.4496714773)21.3:0.0327640091)34.9:0.0275658558)100:0.3805375234)98.9:0.0472817374)44:0.0425570138)91.1:0.0572453428,(GCF_000388175.3:0.0559429001,GCF_000469665.2:0.0769360295)100:0.8993618682)100:0.1083990136,GCF_000014865.1:0.5062345070)100:0.3037501038,((((GCF_001718895.1:0.1268682683,GCF_014142625.1:0.1207627260)100:0.1146677031,GCF_022869645.1:0.3613238389)62.6:0.0495000000,GCF_054182965.1:0.2456298391)100:0.1527321923,GCF_013388375.1:0.3830701212)90.4:0.0634218772)100:0.4301627437)100:0.1815625486,GCF_008369605.1:0.5007466371); 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 /home/runner/work/mitophy/mitophy/work/origin/tree/iqtree.treefile -m "LG+F+G4{0.818962}" --length 10199 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 /home/runner/work/mitophy/mitophy/work/origin/concat.faa --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 /home/runner/work/mitophy/mitophy/work/origin/concat.faa --alisim mimicked_MSA --num-alignments 100 For more information on using AliSim, please visit: www.iqtree.org/doc/AliSim TIME STAMP ---------- Date and time: Sun Aug 16 00:49:44 2026 Total CPU time used: 427.445 seconds (0h:7m:7s) Total wall-clock time used: 107.706 seconds (0h:1m:47s)