(PITG_00009:0.2854866271,PPTG_16673:0.1426933972,(PHYKE_5721:0.2419606625,PHYSO_296552:0.1491886033):0.2065850583);
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: 442963
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 181 amino-acid sites
Number of constant sites: 75 (= 41.4365% of all sites)
Number of invariant (constant or ambiguous constant) sites: 75 (= 41.4365% of all sites)
Number of parsimony informative sites: 10
Number of distinct site patterns: 136
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 -1158.348 2326.697 + 0.302 2327.040 + 0.319 2342.689 + 0.615
JTTDCMut -1159.555 2329.109 + 0.0904 2329.452 + 0.0955 2345.102 + 0.184
JTT+I -1157.681 2327.362 + 0.216 2327.845 + 0.213 2346.553 + 0.0891
JTT+G4 -1158.166 2328.333 + 0.133 2328.816 + 0.131 2347.524 + 0.0548
JTTDCMut+I -1158.847 2329.695 + 0.0674 2330.177 + 0.0664 2348.886 - 0.0278
JTTDCMut+G4 -1159.345 2330.689 - 0.041 2331.172 - 0.0404 2349.880 - 0.0169
JTT+I+G4 -1157.898 2329.796 + 0.0641 2330.443 + 0.0582 2352.185 - 0.00533
JTT+R2 -1158.180 2330.360 - 0.0483 2331.007 - 0.0439 2352.749 - 0.00402
JTTDCMut+I+G4 -1159.050 2332.100 - 0.0203 2332.747 - 0.0184 2354.489 - 0.00168
JTTDCMut+R2 -1159.347 2332.695 - 0.015 2333.342 - 0.0137 2355.084 - 0.00125
Q.pfam -1167.922 2345.844 - 2.1e-05 2346.187 - 2.22e-05 2361.836 - 4.28e-05
Q.pfam+I -1167.606 2347.213 - 1.06e-05 2347.695 - 1.04e-05 2366.404 - 4.36e-06
Q.pfam+G4 -1167.821 2347.641 - 8.55e-06 2348.124 - 8.42e-06 2366.832 - 3.52e-06
LG -1172.045 2354.090 - 3.4e-07 2354.432 - 3.59e-07 2370.082 - 6.93e-07
Q.pfam+R2 -1167.891 2349.783 - 2.93e-06 2350.430 - 2.66e-06 2372.172 - 2.44e-07
Q.pfam+I+G4 -1167.940 2349.881 - 2.79e-06 2350.528 - 2.53e-06 2372.270 - 2.32e-07
LG+I -1171.400 2354.799 - 2.38e-07 2355.282 - 2.35e-07 2373.990 - 9.82e-08
LG+G4 -1171.743 2355.487 - 1.69e-07 2355.970 - 1.67e-07 2374.678 - 6.96e-08
WAG -1174.359 2358.718 - 3.36e-08 2359.061 - 3.55e-08 2374.711 - 6.85e-08
VT -1175.898 2361.797 - 7.21e-09 2362.140 - 7.62e-09 2377.789 - 1.47e-08
WAG+I -1174.071 2360.143 - 1.65e-08 2360.626 - 1.62e-08 2379.334 - 6.79e-09
LG+I+G4 -1171.635 2357.270 - 6.93e-08 2357.917 - 6.29e-08 2379.660 - 5.77e-09
WAG+G4 -1174.299 2360.598 - 1.31e-08 2361.081 - 1.29e-08 2379.789 - 5.4e-09
LG+R2 -1171.738 2357.475 - 6.26e-08 2358.123 - 5.68e-08 2379.865 - 5.2e-09
Dayhoff -1177.572 2365.145 - 1.35e-09 2365.488 - 1.43e-09 2381.137 - 2.75e-09
DCMut -1177.656 2365.312 - 1.24e-09 2365.655 - 1.31e-09 2381.304 - 2.53e-09
VT+I -1175.694 2363.387 - 3.26e-09 2363.870 - 3.21e-09 2382.578 - 1.34e-09
VT+G4 -1175.897 2363.794 - 2.66e-09 2364.276 - 2.62e-09 2382.985 - 1.09e-09
LG+I+R2 -1171.544 2359.088 - 2.79e-08 2359.925 - 2.31e-08 2384.676 - 4.69e-10
Dayhoff+I -1176.845 2365.690 - 1.03e-09 2366.173 - 1.01e-09 2384.881 - 4.24e-10
DCMut+I -1176.943 2365.886 - 9.33e-10 2366.369 - 9.19e-10 2385.077 - 3.84e-10
WAG+R2 -1174.395 2362.790 - 4.39e-09 2363.437 - 3.98e-09 2385.179 - 3.65e-10
WAG+I+G4 -1174.408 2362.815 - 4.33e-09 2363.463 - 3.93e-09 2385.205 - 3.6e-10
Dayhoff+G4 -1177.236 2366.471 - 6.97e-10 2366.954 - 6.86e-10 2385.662 - 2.87e-10
DCMut+G4 -1177.331 2366.662 - 6.33e-10 2367.145 - 6.24e-10 2385.853 - 2.61e-10
VT+I+G4 -1176.015 2366.030 - 8.68e-10 2366.678 - 7.88e-10 2388.420 - 7.22e-11
VT+R2 -1176.028 2366.056 - 8.57e-10 2366.703 - 7.78e-10 2388.445 - 7.13e-11
LG+R3 -1171.680 2361.361 - 8.97e-09 2362.414 - 6.64e-09 2390.147 - 3.04e-11
Dayhoff+I+G4 -1177.086 2368.172 - 2.98e-10 2368.820 - 2.7e-10 2390.562 - 2.47e-11
DCMut+I+G4 -1177.189 2368.378 - 2.68e-10 2369.026 - 2.44e-10 2390.768 - 2.23e-11
Dayhoff+R2 -1177.218 2368.435 - 2.61e-10 2369.083 - 2.37e-10 2390.825 - 2.17e-11
DCMut+R2 -1177.316 2368.632 - 2.36e-10 2369.280 - 2.15e-10 2391.022 - 1.97e-11
LG+I+R3 -1171.512 2363.024 - 3.9e-09 2364.318 - 2.56e-09 2395.009 - 2.68e-12
JTT+F -1145.822 2339.644 - 0.000466 2347.336 - 1.25e-05 2416.408 - 6.04e-17
JTTDCMut+F -1146.774 2341.548 - 0.00018 2349.240 - 4.82e-06 2418.312 - 2.33e-17
PMB -1196.470 2402.940 - 8.39e-18 2403.283 - 8.87e-18 2418.933 - 1.71e-17
JTT+F+I -1144.884 2339.768 - 0.000438 2348.155 - 8.29e-06 2419.730 - 1.15e-17
JTT+F+G4 -1145.591 2341.183 - 0.000216 2349.570 - 4.09e-06 2421.145 - 5.65e-18
JTTDCMut+F+I -1145.806 2341.611 - 0.000174 2349.998 - 3.3e-06 2421.574 - 4.56e-18
JTTDCMut+F+G4 -1146.518 2343.036 - 8.55e-05 2351.423 - 1.62e-06 2422.998 - 2.24e-18
PMB+I -1196.261 2404.522 - 3.8e-18 2405.005 - 3.75e-18 2423.713 - 1.57e-18
PMB+G4 -1196.447 2404.894 - 3.16e-18 2405.377 - 3.11e-18 2424.085 - 1.3e-18
JTT+F+I+G4 -1145.017 2342.035 - 0.000141 2351.151 - 1.85e-06 2425.195 - 7.46e-19
JTT+F+R2 -1145.575 2343.149 - 8.08e-05 2352.266 - 1.06e-06 2426.310 - 4.27e-19
JTTDCMut+F+I+G4 -1145.932 2343.864 - 5.65e-05 2352.981 - 7.42e-07 2427.025 - 2.99e-19
JTTDCMut+F+R2 -1146.492 2344.984 - 3.23e-05 2354.101 - 4.24e-07 2428.145 - 1.71e-19
PMB+R2 -1196.587 2407.174 - 1.01e-18 2407.821 - 9.17e-19 2429.563 - 8.4e-20
PMB+I+G4 -1196.649 2407.297 - 9.5e-19 2407.944 - 8.62e-19 2429.687 - 7.9e-20
Blosum62 -1201.857 2413.714 - 3.84e-20 2414.057 - 4.06e-20 2429.707 - 7.82e-20
Q.pfam+F -1152.950 2353.900 - 3.74e-07 2361.592 - 1e-08 2430.664 - 4.85e-20
Blosum62+I -1201.581 2415.162 - 1.86e-20 2415.645 - 1.83e-20 2434.353 - 7.66e-21
Blosum62+G4 -1201.783 2415.566 - 1.52e-20 2416.049 - 1.5e-20 2434.757 - 6.26e-21
Q.pfam+F+I -1152.419 2354.838 - 2.34e-07 2363.225 - 4.43e-09 2434.800 - 6.13e-21
Q.pfam+F+G4 -1152.845 2355.691 - 1.53e-07 2364.078 - 2.89e-09 2435.653 - 4e-21
LG+F -1156.583 2361.167 - 9.88e-09 2368.859 - 2.65e-10 2437.931 - 1.28e-21
Blosum62+R2 -1201.874 2417.747 - 5.11e-21 2418.395 - 4.64e-21 2440.137 - 4.25e-22
Blosum62+I+G4 -1201.924 2417.847 - 4.86e-21 2418.495 - 4.41e-21 2440.237 - 4.04e-22
Q.pfam+F+I+G4 -1152.706 2357.412 - 6.46e-08 2366.529 - 8.49e-10 2440.573 - 3.42e-22
LG+F+I -1155.402 2360.805 - 1.18e-08 2369.192 - 2.24e-10 2440.767 - 3.1e-22
Q.pfam+F+R2 -1152.903 2357.805 - 5.31e-08 2366.922 - 6.97e-10 2440.966 - 2.81e-22
LG+F+G4 -1156.129 2362.259 - 5.72e-09 2370.646 - 1.08e-10 2442.221 - 1.5e-22
WAG+F -1159.721 2367.443 - 4.28e-10 2375.135 - 1.15e-11 2444.207 - 5.55e-23
LG+F+I+G4 -1155.498 2362.996 - 3.96e-09 2372.113 - 5.2e-11 2446.157 - 2.09e-23
Dayhoff+F -1161.249 2370.498 - 9.3e-11 2378.191 - 2.49e-12 2447.262 - 1.21e-23
LG+F+R2 -1156.061 2364.123 - 2.25e-09 2373.240 - 2.96e-11 2447.284 - 1.19e-23
DCMut+F -1161.305 2370.610 - 8.79e-11 2378.302 - 2.36e-12 2447.374 - 1.14e-23
WAG+F+I -1159.270 2368.541 - 2.47e-10 2376.928 - 4.68e-12 2448.503 - 6.48e-24
VT+F -1162.133 2372.265 - 3.84e-11 2379.957 - 1.03e-12 2449.029 - 4.98e-24
WAG+F+G4 -1159.610 2369.220 - 1.76e-10 2377.607 - 3.34e-12 2449.183 - 4.61e-24
Dayhoff+F+I -1160.408 2370.816 - 7.93e-11 2379.203 - 1.5e-12 2450.779 - 2.08e-24
DCMut+F+I -1160.480 2370.960 - 7.38e-11 2379.347 - 1.4e-12 2450.923 - 1.93e-24
Dayhoff+F+G4 -1160.922 2371.843 - 4.75e-11 2380.230 - 8.99e-13 2451.806 - 1.24e-24
DCMut+F+G4 -1160.989 2371.979 - 4.44e-11 2380.366 - 8.4e-13 2451.941 - 1.16e-24
VT+F+I -1161.773 2373.546 - 2.03e-11 2381.933 - 3.84e-13 2453.509 - 5.31e-25
WAG+F+I+G4 -1159.517 2371.033 - 7.12e-11 2380.150 - 9.35e-13 2454.194 - 3.77e-25
VT+F+G4 -1162.120 2374.239 - 1.43e-11 2382.627 - 2.71e-13 2454.202 - 3.75e-25
WAG+F+R2 -1159.669 2371.338 - 6.11e-11 2380.454 - 8.03e-13 2454.498 - 3.23e-25
Dayhoff+F+I+G4 -1160.598 2373.197 - 2.41e-11 2382.314 - 3.17e-13 2456.358 - 1.28e-25
DCMut+F+I+G4 -1160.675 2373.350 - 2.23e-11 2382.467 - 2.94e-13 2456.511 - 1.18e-25
Dayhoff+F+R2 -1160.906 2373.812 - 1.77e-11 2382.929 - 2.33e-13 2456.973 - 9.38e-26
DCMut+F+R2 -1160.977 2373.954 - 1.65e-11 2383.070 - 2.17e-13 2457.114 - 8.74e-26
VT+F+I+G4 -1162.060 2376.121 - 5.59e-12 2385.237 - 7.35e-14 2459.281 - 2.96e-26
VT+F+R2 -1162.268 2376.535 - 4.54e-12 2385.652 - 5.97e-14 2459.696 - 2.4e-26
PMB+F -1177.273 2402.546 - 1.02e-17 2410.238 - 2.74e-19 2479.310 - 1.32e-30
PMB+F+I -1176.939 2403.879 - 5.25e-18 2412.266 - 9.93e-20 2483.841 - 1.37e-31
PMB+F+G4 -1177.218 2404.437 - 3.97e-18 2412.824 - 7.52e-20 2484.399 - 1.04e-31
Blosum62+F -1180.685 2409.369 - 3.37e-19 2417.062 - 9.03e-21 2486.133 - 4.37e-32
PMB+F+I+G4 -1177.232 2406.464 - 1.44e-18 2415.581 - 1.89e-20 2489.625 - 7.62e-33
PMB+F+R2 -1177.321 2406.642 - 1.32e-18 2415.759 - 1.73e-20 2489.803 - 6.98e-33
Blosum62+F+I -1180.095 2410.191 - 2.24e-19 2418.578 - 4.23e-21 2490.153 - 5.85e-33
Blosum62+F+G4 -1180.486 2410.973 - 1.51e-19 2419.360 - 2.86e-21 2490.935 - 3.96e-33
Blosum62+F+I+G4 -1180.337 2412.673 - 6.46e-20 2421.790 - 8.49e-22 2495.834 - 3.42e-34
Blosum62+F+R2 -1180.509 2413.017 - 5.44e-20 2422.134 - 7.15e-22 2496.178 - 2.88e-34
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: -1158.3484 (s.e. 36.1340)
Unconstrained log-likelihood (without tree): -860.1449
Number of free parameters (#branches + #model parameters): 5
Akaike information criterion (AIC) score: 2326.6967
Corrected Akaike information criterion (AICc) score: 2327.0396
Bayesian information criterion (BIC) score: 2342.6892
Total tree length (sum of branch lengths): 1.0259
Sum of internal branch lengths: 0.2066 (20.1367% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'PITG_00009' is drawn at root
+-------------------------------------PITG_00009
|
+------------------PPTG_16673
|
| +-------------------------------PHYKE_5721
+--------------------------|
+------------------PHYSO_296552
Tree in newick format:
(PITG_00009:0.2854866271,PPTG_16673:0.1426933972,(PHYKE_5721:0.2419606625,PHYSO_296552:0.1491886033):0.2065850583);
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 181
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 16:23:20 2023
Total CPU time used: 0.609509 seconds (0h:0m:0s)
Total wall-clock time used: 0.232663 seconds (0h:0m:0s)