(PPTG_07932:0.5753178220,(PITG_00010:0.1002062857,(H257_06152:0.5272166993,(SPRG_08854:0.0612878654,SDRG_13678:0.0000027130):0.3685962798):0.9529733402):0.1440895346,PHYCA_131593:0.0722745277);
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: 600079
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: 6 sequences with 150 amino-acid sites
Number of constant sites: 32 (= 21.3333% of all sites)
Number of invariant (constant or ambiguous constant) sites: 32 (= 21.3333% of all sites)
Number of parsimony informative sites: 68
Number of distinct site patterns: 131
ModelFinder
-----------
Best-fit model according to BIC: Q.pfam+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
Q.pfam+G4 -1415.663 2851.326 + 0.126 2852.909 + 0.609 2881.432 + 0.831
Q.pfam+R2 -1415.500 2853.000 + 0.0545 2854.914 + 0.224 2886.117 + 0.0798
Q.pfam+I+G4 -1416.067 2854.134 - 0.0309 2856.047 + 0.127 2887.251 - 0.0453
Q.pfam+I -1418.861 2857.723 - 0.00514 2859.305 - 0.0249 2887.829 - 0.0339
LG+G4 -1420.287 2860.574 - 0.00124 2862.157 - 0.00598 2890.680 - 0.00815
LG+R2 -1420.110 2862.219 - 0.000543 2864.132 - 0.00223 2895.336 - 0.000795
LG+I+G4 -1420.629 2863.257 - 0.000323 2865.170 - 0.00132 2896.374 - 0.000473
WAG+G4 -1423.841 2867.682 - 3.54e-05 2869.265 - 0.000171 2897.788 - 0.000233
LG+I -1423.860 2867.720 - 3.47e-05 2869.303 - 0.000168 2897.826 - 0.000229
LG+I+R2 -1420.280 2864.561 - 0.000168 2866.838 - 0.000575 2900.688 - 5.47e-05
WAG+R2 -1423.662 2869.325 - 1.56e-05 2871.238 - 6.38e-05 2902.442 - 2.28e-05
WAG+I -1426.333 2872.666 - 2.93e-06 2874.249 - 1.42e-05 2902.772 - 1.93e-05
WAG+I+G4 -1424.040 2870.080 - 1.07e-05 2871.993 - 4.37e-05 2903.197 - 1.56e-05
LG -1429.063 2876.127 - 5.19e-07 2877.412 - 2.91e-06 2903.222 - 1.54e-05
VT+G4 -1427.099 2874.198 - 1.36e-06 2875.781 - 6.58e-06 2904.305 - 8.97e-06
LG+R3 -1420.211 2866.421 - 6.64e-05 2869.098 - 0.000186 2905.560 - 4.79e-06
JTT+G4 -1428.875 2877.749 - 2.3e-07 2879.332 - 1.11e-06 2907.856 - 1.52e-06
JTTDCMut+G4 -1429.031 2878.062 - 1.97e-07 2879.645 - 9.53e-07 2908.169 - 1.3e-06
VT+I -1429.120 2878.240 - 1.8e-07 2879.823 - 8.72e-07 2908.347 - 1.19e-06
VT+R2 -1426.957 2875.913 - 5.77e-07 2877.826 - 2.37e-06 2909.030 - 8.45e-07
VT+I+G4 -1427.390 2876.780 - 3.74e-07 2878.693 - 1.53e-06 2909.897 - 5.48e-07
LG+I+R3 -1420.365 2868.731 - 2.09e-05 2871.842 - 4.71e-05 2910.880 - 3.35e-07
JTT+R2 -1428.640 2879.280 - 1.07e-07 2881.193 - 4.39e-07 2912.397 - 1.57e-07
JTTDCMut+R2 -1428.815 2879.629 - 9e-08 2881.542 - 3.69e-07 2912.746 - 1.32e-07
JTT+I+G4 -1429.228 2880.457 - 5.95e-08 2882.370 - 2.44e-07 2913.574 - 8.71e-08
JTTDCMut+I+G4 -1429.375 2880.749 - 5.14e-08 2882.662 - 2.11e-07 2913.866 - 7.53e-08
Dayhoff+G4 -1431.907 2883.814 - 1.11e-08 2885.397 - 5.37e-08 2913.920 - 7.33e-08
DCMut+G4 -1431.950 2883.900 - 1.06e-08 2885.482 - 5.14e-08 2914.006 - 7.02e-08
JTT+I -1432.504 2885.008 - 6.12e-09 2886.590 - 2.96e-08 2915.114 - 4.03e-08
JTTDCMut+I -1432.645 2885.290 - 5.31e-09 2886.873 - 2.57e-08 2915.397 - 3.5e-08
Dayhoff+R2 -1431.772 2885.544 - 4.68e-09 2887.457 - 1.92e-08 2918.661 - 6.85e-09
DCMut+R2 -1431.819 2885.637 - 4.46e-09 2887.550 - 1.83e-08 2918.754 - 6.53e-09
Dayhoff+I+G4 -1432.257 2886.513 - 2.88e-09 2888.426 - 1.18e-08 2919.630 - 4.22e-09
DCMut+I+G4 -1432.301 2886.601 - 2.76e-09 2888.514 - 1.13e-08 2919.718 - 4.04e-09
Dayhoff+I -1435.454 2890.907 - 3.2e-10 2892.490 - 1.55e-09 2921.014 - 2.11e-09
DCMut+I -1435.468 2890.936 - 3.16e-10 2892.519 - 1.53e-09 2921.042 - 2.08e-09
PMB+G4 -1437.390 2894.780 - 4.62e-11 2896.363 - 2.23e-10 2924.886 - 3.05e-10
PMB+I -1439.087 2898.174 - 8.46e-12 2899.757 - 4.09e-11 2928.281 - 5.58e-11
Blosum62+G4 -1439.508 2899.015 - 5.56e-12 2900.598 - 2.69e-11 2929.122 - 3.66e-11
PMB+R2 -1437.159 2896.318 - 2.14e-11 2898.231 - 8.77e-11 2929.435 - 3.13e-11
PMB+I+G4 -1437.581 2897.163 - 1.4e-11 2899.076 - 5.75e-11 2930.280 - 2.05e-11
Blosum62+I -1441.677 2903.353 - 6.35e-13 2904.936 - 3.07e-12 2933.460 - 4.19e-12
Blosum62+R2 -1439.326 2900.652 - 2.45e-12 2902.565 - 1e-11 2933.769 - 3.59e-12
Blosum62+I+G4 -1439.825 2901.651 - 1.49e-12 2903.564 - 6.1e-12 2934.768 - 2.18e-12
Q.pfam+F+G4 -1395.504 2849.008 + 0.402 2863.508 - 0.00304 2936.316 - 1e-12
LG+F+G4 -1397.539 2853.079 + 0.0524 2867.579 - 0.000397 2940.387 - 1.31e-13
Q.pfam+F+R2 -1395.339 2850.678 + 0.174 2866.308 - 0.00075 2940.997 - 9.67e-14
Q.pfam+F+I+G4 -1395.987 2851.973 + 0.0911 2867.604 - 0.000392 2942.293 - 5.06e-14
Q.pfam+F+I -1399.133 2856.267 - 0.0107 2870.767 - 8.07e-05 2943.575 - 2.66e-14
LG+F+R2 -1397.392 2854.785 - 0.0224 2870.415 - 9.62e-05 2945.104 - 1.24e-14
Dayhoff+F+G4 -1400.154 2858.309 - 0.00384 2872.809 - 2.91e-05 2945.617 - 9.59e-15
DCMut+F+G4 -1400.164 2858.327 - 0.0038 2872.827 - 2.88e-05 2945.636 - 9.51e-15
LG+F+I+G4 -1397.997 2855.994 - 0.0122 2871.624 - 5.26e-05 2946.313 - 6.78e-15
WAG+F+G4 -1401.092 2860.184 - 0.0015 2874.684 - 1.14e-05 2947.492 - 3.76e-15
LG+F+I -1401.899 2861.798 - 0.00067 2876.298 - 5.08e-06 2949.107 - 1.68e-15
Dayhoff+F+R2 -1400.123 2860.247 - 0.00146 2875.877 - 6.27e-06 2950.566 - 8.08e-16
DCMut+F+R2 -1400.135 2860.270 - 0.00144 2875.900 - 6.2e-06 2950.589 - 7.99e-16
Dayhoff+F+I+G4 -1400.406 2860.813 - 0.0011 2876.443 - 4.72e-06 2951.132 - 6.09e-16
DCMut+F+I+G4 -1400.419 2860.838 - 0.00108 2876.468 - 4.66e-06 2951.157 - 6.01e-16
DCMut+F+I -1403.469 2864.938 - 0.000139 2879.438 - 1.06e-06 2952.246 - 3.49e-16
WAG+F+R2 -1400.965 2861.930 - 0.000628 2877.560 - 2.7e-06 2952.249 - 3.48e-16
Dayhoff+F+I -1403.485 2864.970 - 0.000137 2879.470 - 1.04e-06 2952.279 - 3.43e-16
WAG+F+I+G4 -1401.452 2862.903 - 0.000386 2878.534 - 1.66e-06 2953.223 - 2.14e-16
VT+F+G4 -1404.059 2866.118 - 7.73e-05 2880.618 - 5.86e-07 2953.427 - 1.93e-16
WAG+F+I -1404.422 2866.843 - 5.38e-05 2881.343 - 4.08e-07 2954.151 - 1.35e-16
JTTDCMut+F+G4 -1405.604 2869.209 - 1.65e-05 2883.709 - 1.25e-07 2956.517 - 4.12e-17
JTT+F+G4 -1405.982 2869.964 - 1.13e-05 2884.464 - 8.56e-08 2957.273 - 2.83e-17
VT+F+R2 -1403.956 2867.912 - 3.15e-05 2883.543 - 1.36e-07 2958.231 - 1.75e-17
VT+F+I -1406.645 2871.289 - 5.83e-06 2885.789 - 4.41e-08 2958.598 - 1.46e-17
VT+F+I+G4 -1404.487 2868.973 - 1.85e-05 2884.603 - 7.98e-08 2959.292 - 1.03e-17
JTTDCMut+F+R2 -1405.494 2870.989 - 6.77e-06 2886.619 - 2.91e-08 2961.308 - 3.76e-18
JTT+F+R2 -1405.858 2871.715 - 4.71e-06 2887.346 - 2.03e-08 2962.034 - 2.61e-18
JTTDCMut+F+I+G4 -1406.011 2872.022 - 4.04e-06 2887.653 - 1.74e-08 2962.341 - 2.24e-18
JTT+F+I+G4 -1406.402 2872.805 - 2.73e-06 2888.435 - 1.18e-08 2963.124 - 1.52e-18
JTTDCMut+F+I -1409.565 2877.130 - 3.14e-07 2891.630 - 2.38e-09 2964.439 - 7.85e-19
JTT+F+I -1409.963 2877.925 - 2.11e-07 2892.425 - 1.6e-09 2965.234 - 5.28e-19
Blosum62+F+G4 -1410.179 2878.357 - 1.7e-07 2892.857 - 1.29e-09 2965.666 - 4.25e-19
PMB+F+G4 -1410.183 2878.366 - 1.69e-07 2892.866 - 1.28e-09 2965.675 - 4.23e-19
PMB+F+R2 -1410.045 2880.090 - 7.15e-08 2895.720 - 3.08e-10 2970.409 - 3.97e-20
Blosum62+F+R2 -1410.051 2880.101 - 7.11e-08 2895.731 - 3.06e-10 2970.420 - 3.95e-20
PMB+F+I -1412.811 2883.622 - 1.22e-08 2898.122 - 9.26e-11 2970.930 - 3.06e-20
PMB+F+I+G4 -1410.597 2881.194 - 4.12e-08 2896.824 - 1.77e-10 2971.513 - 2.28e-20
Blosum62+F+I+G4 -1410.612 2881.223 - 4.06e-08 2896.853 - 1.75e-10 2971.542 - 2.25e-20
Blosum62+F+I -1413.362 2884.723 - 7.05e-09 2899.223 - 5.34e-11 2972.032 - 1.76e-20
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: Q.pfam+G4
State frequencies: (model)
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 1.9142
Category Relative_rate Proportion
1 0.2828 0.2500
2 0.6456 0.2500
3 1.0677 0.2500
4 2.0039 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: -1415.6628 (s.e. 47.1305)
Unconstrained log-likelihood (without tree): -716.1620
Number of free parameters (#branches + #model parameters): 10
Akaike information criterion (AIC) score: 2851.3255
Corrected Akaike information criterion (AICc) score: 2852.9082
Bayesian information criterion (BIC) score: 2881.4319
Total tree length (sum of branch lengths): 2.8020
Sum of internal branch lengths: 1.4657 (52.3083% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'PPTG_07932' is drawn at root
+--------------------PPTG_07932
|
| +--PITG_00010
+----|
| | +------------------H257_06152
| +----------------------------------|
| | +--SPRG_08854
| +------------|
| +**SDRG_13678
|
+--PHYCA_131593
Tree in newick format:
(PPTG_07932:0.5753178220,(PITG_00010:0.1002062857,(H257_06152:0.5272166993,(SPRG_08854:0.0612878654,SDRG_13678:0.0000027130):0.3685962798):0.9529733402):0.1440895346,PHYCA_131593:0.0722745277);
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 "Q.pfam+G4{1.91418}" --length 150
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: Fri Apr 26 06:33:03 2024
Total CPU time used: 4.05966 seconds (0h:0m:4s)
Total wall-clock time used: 1.40933 seconds (0h:0m:1s)