(PHYSO_530254:1.4460714602,HYAP_01510:0.4581642521,(PHYCA_104429:0.0000020017,PHYRA_51904:0.0000024082):0.1085518870);
Protein sequences → MUSCLE → trimAl (automated1) → IQ-TREE (Automatic model selection using ModelFinder)
Root the phylogeny or hide taxa by clicking on nodes
Phylogeny (unrooted) rendered using phylotree.js
Reconstruct this phylogeny using PHYLIP Neighbor, FastTree, IQ-TREE (+ ModelFinder) or PhyML?
IQ-TREE 2.2.0.8 COVID-edition built Oct 4 2022
Input file name: seq.aln-trimal
Type of analysis: ModelFinder + tree reconstruction
Random seed number: 871908
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
SEQUENCE ALIGNMENT
------------------
Input data: 4 sequences with 93 amino-acid sites
Number of constant sites: 24 (= 25.8065% of all sites)
Number of invariant (constant or ambiguous constant) sites: 24 (= 25.8065% of all sites)
Number of parsimony informative sites: 1
Number of distinct site patterns: 83
ModelFinder
-----------
Best-fit model according to BIC: JTT
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
JTT -564.478 1138.957 + 0.289 1139.646 + 0.32 1151.620 + 0.482
JTTDCMut -565.091 1140.182 + 0.157 1140.872 + 0.173 1152.845 + 0.261
VT -566.383 1142.767 - 0.043 1143.456 - 0.0476 1155.430 + 0.0718
JTT+I -564.455 1140.911 + 0.109 1141.887 + 0.104 1156.106 + 0.0512
JTT+G4 -564.527 1141.054 + 0.101 1142.031 + 0.097 1156.250 - 0.0476
JTTDCMut+I -565.085 1142.169 + 0.058 1143.146 + 0.0555 1157.365 - 0.0273
JTTDCMut+G4 -565.127 1142.254 + 0.0556 1143.231 + 0.0532 1157.450 - 0.0261
VT+I -566.369 1144.738 - 0.016 1145.715 - 0.0154 1159.934 - 0.00755
VT+G4 -566.507 1145.013 - 0.014 1145.990 - 0.0134 1160.209 - 0.00658
JTT+R2 -564.459 1142.918 - 0.0399 1144.235 - 0.0322 1160.646 - 0.00529
JTT+I+G4 -564.738 1143.475 - 0.0302 1144.793 - 0.0244 1161.203 - 0.004
JTTDCMut+R2 -565.054 1144.108 - 0.022 1145.425 - 0.0178 1161.836 - 0.00292
JTTDCMut+I+G4 -565.343 1144.686 - 0.0165 1146.003 - 0.0133 1162.414 - 0.00218
VT+R2 -566.577 1147.153 - 0.0048 1148.471 - 0.00388 1164.881 - 0.000636
VT+I+G4 -566.628 1147.256 - 0.00456 1148.573 - 0.00368 1164.984 - 0.000604
JTT+I+R2 -564.451 1144.901 - 0.0148 1146.615 - 0.0098 1165.162 - 0.000553
Q.pfam -571.535 1153.071 - 0.000249 1153.760 - 0.000275 1165.734 - 0.000415
JTTDCMut+I+R2 -565.039 1146.077 - 0.00821 1147.791 - 0.00544 1166.338 - 0.000307
WAG -571.987 1153.975 - 0.000158 1154.664 - 0.000175 1166.638 - 0.000264
Q.pfam+G4 -570.112 1152.223 - 0.00038 1153.200 - 0.000364 1167.419 - 0.000179
DCMut -573.176 1156.351 - 4.83e-05 1157.041 - 5.34e-05 1169.014 - 8.06e-05
LG -573.197 1156.395 - 4.72e-05 1157.085 - 5.22e-05 1169.058 - 7.88e-05
Dayhoff -573.223 1156.446 - 4.6e-05 1157.136 - 5.09e-05 1169.109 - 7.68e-05
Q.pfam+R2 -568.698 1151.395 - 0.000575 1152.713 - 0.000465 1169.123 - 7.63e-05
JTT+R3 -564.218 1146.437 - 0.00686 1148.606 - 0.00362 1169.230 - 7.23e-05
VT+I+R2 -566.607 1149.214 - 0.00171 1150.929 - 0.00113 1169.475 - 6.4e-05
Q.pfam+I -571.147 1154.294 - 0.000135 1155.271 - 0.000129 1169.489 - 6.35e-05
LG+G4 -571.223 1154.445 - 0.000125 1155.422 - 0.00012 1169.641 - 5.89e-05
LG+R2 -569.011 1152.023 - 0.00042 1153.340 - 0.00034 1169.751 - 5.57e-05
JTTDCMut+R3 -564.776 1147.551 - 0.00393 1149.720 - 0.00208 1170.345 - 4.14e-05
WAG+R2 -569.647 1153.294 - 0.000223 1154.612 - 0.00018 1171.022 - 2.95e-05
WAG+I -571.976 1155.951 - 5.89e-05 1156.928 - 5.65e-05 1171.147 - 2.77e-05
WAG+G4 -572.153 1156.306 - 4.94e-05 1157.282 - 4.73e-05 1171.501 - 2.32e-05
PMB -574.542 1159.084 - 1.23e-05 1159.774 - 1.36e-05 1171.747 - 2.05e-05
Q.pfam+I+G4 -570.356 1154.712 - 0.00011 1156.030 - 8.85e-05 1172.440 - 1.45e-05
DCMut+G4 -572.642 1157.283 - 3.03e-05 1158.260 - 2.9e-05 1172.479 - 1.42e-05
Dayhoff+G4 -572.656 1157.311 - 2.99e-05 1158.288 - 2.86e-05 1172.507 - 1.41e-05
LG+I -572.885 1157.771 - 2.37e-05 1158.747 - 2.27e-05 1172.966 - 1.12e-05
VT+R3 -566.211 1150.422 - 0.000936 1152.590 - 0.000494 1173.215 - 9.86e-06
DCMut+I -573.174 1158.348 - 1.78e-05 1159.325 - 1.7e-05 1173.544 - 8.37e-06
Q.pfam+I+R2 -568.673 1153.346 - 0.000217 1155.061 - 0.000144 1173.607 - 8.11e-06
Dayhoff+I -573.222 1158.444 - 1.7e-05 1159.421 - 1.62e-05 1173.639 - 7.98e-06
DCMut+R2 -571.015 1156.030 - 5.67e-05 1157.347 - 4.58e-05 1173.758 - 7.52e-06
Blosum62 -575.558 1161.115 - 4.46e-06 1161.805 - 4.93e-06 1173.778 - 7.44e-06
Dayhoff+R2 -571.072 1156.145 - 5.35e-05 1157.462 - 4.32e-05 1173.873 - 7.1e-06
LG+I+R2 -569.095 1154.189 - 0.000142 1155.904 - 9.43e-05 1174.450 - 5.32e-06
LG+I+G4 -571.529 1157.057 - 3.39e-05 1158.375 - 2.74e-05 1174.786 - 4.5e-06
WAG+I+R2 -569.657 1155.314 - 8.11e-05 1157.029 - 5.37e-05 1175.575 - 3.03e-06
WAG+I+G4 -572.248 1158.496 - 1.65e-05 1159.814 - 1.33e-05 1176.224 - 2.19e-06
PMB+I -574.522 1161.044 - 4.62e-06 1162.021 - 4.43e-06 1176.239 - 2.17e-06
PMB+G4 -574.616 1161.232 - 4.21e-06 1162.209 - 4.03e-06 1176.427 - 1.98e-06
DCMut+I+G4 -572.889 1159.778 - 8.7e-06 1161.096 - 7.03e-06 1177.507 - 1.15e-06
Dayhoff+I+G4 -572.905 1159.810 - 8.56e-06 1161.127 - 6.92e-06 1177.538 - 1.14e-06
Q.pfam+R3 -568.651 1155.302 - 8.16e-05 1157.471 - 4.31e-05 1178.095 - 8.59e-07
Blosum62+I -575.510 1163.021 - 1.72e-06 1163.997 - 1.65e-06 1178.216 - 8.09e-07
Dayhoff+I+R2 -571.051 1158.102 - 2.01e-05 1159.816 - 1.33e-05 1178.363 - 7.52e-07
DCMut+I+R2 -571.062 1158.125 - 1.99e-05 1159.839 - 1.32e-05 1178.386 - 7.43e-07
Blosum62+G4 -575.714 1163.429 - 1.4e-06 1164.405 - 1.34e-06 1178.624 - 6.6e-07
LG+R3 -569.006 1156.011 - 5.72e-05 1158.180 - 3.02e-05 1178.805 - 6.03e-07
WAG+R3 -569.629 1157.257 - 3.07e-05 1159.426 - 1.62e-05 1180.051 - 3.23e-07
PMB+R2 -574.683 1163.365 - 1.45e-06 1164.683 - 1.17e-06 1181.093 - 1.92e-07
PMB+I+G4 -574.785 1163.569 - 1.31e-06 1164.887 - 1.06e-06 1181.298 - 1.73e-07
Dayhoff+R3 -570.960 1159.920 - 8.1e-06 1162.088 - 4.28e-06 1182.713 - 8.54e-08
DCMut+R3 -570.964 1159.928 - 8.07e-06 1162.097 - 4.26e-06 1182.722 - 8.5e-08
Blosum62+R2 -575.545 1165.090 - 6.11e-07 1166.407 - 4.94e-07 1182.818 - 8.1e-08
Blosum62+I+G4 -575.764 1165.527 - 4.91e-07 1166.845 - 3.97e-07 1183.255 - 6.51e-08
LG+I+R3 -569.026 1158.051 - 2.06e-05 1160.734 - 8.42e-06 1183.377 - 6.13e-08
Blosum62+I+R2 -574.730 1165.459 - 5.08e-07 1167.174 - 3.37e-07 1185.720 - 1.9e-08
PMB+I+R2 -574.743 1165.486 - 5.01e-07 1167.200 - 3.32e-07 1185.746 - 1.87e-08
PMB+R3 -574.517 1167.033 - 2.31e-07 1169.202 - 1.22e-07 1189.827 - 2.44e-09
Blosum62+R3 -574.646 1167.292 - 2.03e-07 1169.461 - 1.07e-07 1190.086 - 2.14e-09
JTT+F -555.640 1159.280 - 1.12e-05 1176.927 - 2.57e-09 1220.062 - 6.62e-16
JTTDCMut+F -556.094 1160.189 - 7.08e-06 1177.836 - 1.63e-09 1220.971 - 4.21e-16
JTT+F+G4 -555.451 1160.901 - 4.96e-06 1180.304 - 4.74e-10 1224.216 - 8.3e-17
JTT+F+I -555.613 1161.227 - 4.22e-06 1180.630 - 4.03e-10 1224.542 - 7.06e-17
JTTDCMut+F+G4 -555.857 1161.714 - 3.3e-06 1181.117 - 3.16e-10 1225.029 - 5.53e-17
JTTDCMut+F+I -556.064 1162.129 - 2.69e-06 1181.532 - 2.57e-10 1225.444 - 4.49e-17
VT+F -558.712 1165.424 - 5.17e-07 1183.071 - 1.19e-10 1226.206 - 3.07e-17
DCMut+F -559.833 1167.666 - 1.69e-07 1185.313 - 3.88e-11 1228.448 - 1e-17
Dayhoff+F -559.887 1167.774 - 1.6e-07 1185.421 - 3.67e-11 1228.556 - 9.48e-18
JTT+F+R2 -555.376 1162.753 - 1.97e-06 1184.025 - 7.38e-11 1228.600 - 9.27e-18
JTT+F+I+G4 -555.686 1163.372 - 1.44e-06 1184.645 - 5.41e-11 1229.220 - 6.8e-18
JTTDCMut+F+R2 -555.765 1163.529 - 1.33e-06 1184.802 - 5e-11 1229.377 - 6.29e-18
JTTDCMut+F+I+G4 -556.092 1164.184 - 9.61e-07 1185.457 - 3.61e-11 1230.032 - 4.53e-18
VT+F+I -558.713 1167.426 - 1.9e-07 1186.829 - 1.82e-11 1230.741 - 3.18e-18
VT+F+G4 -559.016 1168.033 - 1.4e-07 1187.436 - 1.34e-11 1231.348 - 2.35e-18
DCMut+F+G4 -559.075 1168.150 - 1.32e-07 1187.552 - 1.26e-11 1231.464 - 2.21e-18
Dayhoff+F+G4 -559.096 1168.192 - 1.3e-07 1187.595 - 1.24e-11 1231.507 - 2.17e-18
PMB+F -561.454 1170.909 - 3.33e-08 1188.556 - 7.66e-12 1231.691 - 1.98e-18
Dayhoff+F+R2 -556.946 1165.891 - 4.09e-07 1187.164 - 1.54e-11 1231.739 - 1.93e-18
DCMut+F+R2 -556.951 1165.901 - 4.07e-07 1187.174 - 1.53e-11 1231.749 - 1.92e-18
WAG+F -561.649 1171.297 - 2.74e-08 1188.944 - 6.3e-12 1232.080 - 1.63e-18
Q.pfam+F -561.868 1171.735 - 2.2e-08 1189.382 - 5.06e-12 1232.518 - 1.31e-18
JTT+F+I+R2 -555.178 1164.356 - 8.82e-07 1187.617 - 1.22e-11 1232.736 - 1.17e-18
DCMut+F+I -559.825 1169.651 - 6.25e-08 1189.054 - 5.97e-12 1232.966 - 1.05e-18
Dayhoff+F+I -559.879 1169.759 - 5.92e-08 1189.162 - 5.65e-12 1233.074 - 9.9e-19
JTTDCMut+F+I+R2 -555.506 1165.011 - 6.35e-07 1188.273 - 8.82e-12 1233.392 - 8.45e-19
LG+F+R2 -557.945 1167.891 - 1.51e-07 1189.164 - 5.65e-12 1233.738 - 7.1e-19
Q.pfam+F+G4 -560.375 1170.750 - 3.6e-08 1190.153 - 3.44e-12 1234.065 - 6.03e-19
Q.pfam+F+R2 -558.259 1168.518 - 1.1e-07 1189.790 - 4.13e-12 1234.365 - 5.19e-19
WAG+F+R2 -558.261 1168.521 - 1.1e-07 1189.794 - 4.12e-12 1234.369 - 5.18e-19
LG+F -562.852 1173.703 - 8.24e-09 1191.350 - 1.89e-12 1234.485 - 4.89e-19
LG+F+G4 -560.784 1171.567 - 2.4e-08 1190.970 - 2.29e-12 1234.882 - 4.01e-19
VT+F+R2 -558.862 1169.724 - 6.02e-08 1190.997 - 2.26e-12 1235.572 - 2.84e-19
VT+F+I+G4 -559.025 1170.049 - 5.12e-08 1191.322 - 1.92e-12 1235.897 - 2.41e-19
Blosum62+F -563.691 1175.381 - 3.56e-09 1193.028 - 8.18e-13 1236.164 - 2.11e-19
PMB+F+I -561.454 1172.908 - 1.23e-08 1192.311 - 1.17e-12 1236.223 - 2.05e-19
Dayhoff+F+I+R2 -556.966 1167.932 - 1.48e-07 1191.194 - 2.05e-12 1236.312 - 1.96e-19
DCMut+F+I+R2 -556.970 1167.939 - 1.47e-07 1191.201 - 2.04e-12 1236.319 - 1.95e-19
DCMut+F+I+G4 -559.322 1170.644 - 3.8e-08 1191.917 - 1.43e-12 1236.492 - 1.79e-19
WAG+F+G4 -561.590 1173.180 - 1.07e-08 1192.583 - 1.02e-12 1236.495 - 1.79e-19
JTT+F+R3 -554.804 1165.609 - 4.71e-07 1190.984 - 2.27e-12 1236.522 - 1.77e-19
Dayhoff+F+I+G4 -559.344 1170.689 - 3.72e-08 1191.962 - 1.39e-12 1236.537 - 1.75e-19
WAG+F+I -561.645 1173.290 - 1.01e-08 1192.693 - 9.68e-13 1236.605 - 1.69e-19
Q.pfam+F+I -561.669 1173.338 - 9.88e-09 1192.741 - 9.44e-13 1236.653 - 1.65e-19
PMB+F+G4 -561.785 1173.571 - 8.8e-09 1192.974 - 8.41e-13 1236.886 - 1.47e-19
JTTDCMut+F+R3 -555.093 1166.187 - 3.53e-07 1191.562 - 1.7e-12 1237.099 - 1.32e-19
VT+F+I+R2 -557.942 1169.885 - 5.56e-08 1193.146 - 7.71e-13 1238.265 - 7.39e-20
LG+F+I+R2 -558.042 1170.084 - 5.03e-08 1193.345 - 6.98e-13 1238.464 - 6.69e-20
LG+F+I -562.759 1175.518 - 3.32e-09 1194.921 - 3.18e-13 1238.833 - 5.56e-20
WAG+F+I+R2 -558.245 1170.490 - 4.11e-08 1193.751 - 5.7e-13 1238.870 - 5.46e-20
Q.pfam+F+I+R2 -558.303 1170.606 - 3.87e-08 1193.867 - 5.38e-13 1238.986 - 5.15e-20
Q.pfam+F+I+G4 -560.627 1173.254 - 1.03e-08 1194.527 - 3.87e-13 1239.102 - 4.86e-20
LG+F+I+G4 -560.986 1173.972 - 7.2e-09 1195.245 - 2.7e-13 1239.820 - 3.4e-20
Blosum62+F+I -563.690 1177.380 - 1.31e-09 1196.783 - 1.25e-13 1240.695 - 2.19e-20
DCMut+F+R3 -556.927 1169.853 - 5.64e-08 1195.228 - 2.72e-13 1240.766 - 2.12e-20
Dayhoff+F+R3 -556.983 1169.965 - 5.34e-08 1195.340 - 2.58e-13 1240.878 - 2e-20
PMB+F+R2 -561.592 1175.184 - 3.93e-09 1196.457 - 1.47e-13 1241.032 - 1.85e-20
Blosum62+F+G4 -563.939 1177.878 - 1.02e-09 1197.281 - 9.76e-14 1241.193 - 1.71e-20
WAG+F+I+G4 -561.801 1175.602 - 3.19e-09 1196.875 - 1.2e-13 1241.450 - 1.5e-20
PMB+F+I+G4 -561.858 1175.717 - 3.01e-09 1196.990 - 1.13e-13 1241.564 - 1.42e-20
Blosum62+F+R2 -561.993 1175.987 - 2.63e-09 1197.260 - 9.86e-14 1241.835 - 1.24e-20
VT+F+R3 -557.897 1171.793 - 2.14e-08 1197.168 - 1.03e-13 1242.706 - 8.02e-21
LG+F+R3 -557.907 1171.814 - 2.12e-08 1197.189 - 1.02e-13 1242.727 - 7.94e-21
WAG+F+R3 -558.212 1172.424 - 1.56e-08 1197.799 - 7.53e-14 1243.336 - 5.85e-21
Q.pfam+F+R3 -558.262 1172.524 - 1.48e-08 1197.899 - 7.16e-14 1243.437 - 5.57e-21
PMB+F+I+R2 -560.685 1175.369 - 3.58e-09 1198.631 - 4.97e-14 1243.750 - 4.76e-21
Blosum62+F+I+G4 -564.100 1180.199 - 3.2e-10 1201.472 - 1.2e-14 1246.047 - 1.51e-21
Blosum62+F+I+R2 -562.077 1178.153 - 8.9e-10 1201.415 - 1.24e-14 1246.534 - 1.18e-21
PMB+F+R3 -560.592 1177.184 - 1.44e-09 1202.559 - 6.97e-15 1248.097 - 5.41e-22
Blosum62+F+R3 -562.011 1180.023 - 3.49e-10 1205.398 - 1.69e-15 1250.935 - 1.31e-22
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: JTT
State frequencies: (model)
Model of rate heterogeneity: Uniform
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -564.4548 (s.e. 17.0692)
Unconstrained log-likelihood (without tree): -407.6688
Number of free parameters (#branches + #model parameters): 5
Akaike information criterion (AIC) score: 1138.9096
Corrected Akaike information criterion (AICc) score: 1139.5993
Bayesian information criterion (BIC) score: 1151.5726
Total tree length (sum of branch lengths): 2.0128
Sum of internal branch lengths: 0.0000 (0.0000% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'PHYSO_530254' is drawn at root
+-----------------------------------------------------------PHYSO_530254
|
+------------------HYAP_01510
|
| +**PHYCA_104429
+---|
+**PHYRA_51904
Tree in newick format:
(PHYSO_530254:1.4460714602,HYAP_01510:0.4581642521,(PHYCA_104429:0.0000020017,PHYRA_51904:0.0000024082):0.1085518870);
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 seq.aln-trimal.treefile -m "JTT" --length 93
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 seq.aln-trimal --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 seq.aln-trimal --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 May 28 16:41:55 2023
Total CPU time used: 0.473024 seconds (0h:0m:0s)
Total wall-clock time used: 0.187249 seconds (0h:0m:0s)