Newick Format
(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 Log
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: 566638

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           -1156.062    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    2373.953 - 1.65e-11    2383.070 - 2.17e-13    2457.114 - 8.75e-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: Tue Apr 16 13:46:45 2024
Total CPU time used: 0.772815 seconds (0h:0m:0s)
Total wall-clock time used: 0.30773 seconds (0h:0m:0s)