(PYAP_22273:0.1518991454,PYAR_24096:0.1921751589,(PYIW_18788:0.6101885954,PYU1_G001739:0.1879670795):0.5113836347);
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: 953258
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 242 amino-acid sites
Number of constant sites: 65 (= 26.8595% of all sites)
Number of invariant (constant or ambiguous constant) sites: 65 (= 26.8595% of all sites)
Number of parsimony informative sites: 37
Number of distinct site patterns: 190
ModelFinder
-----------
Best-fit model according to BIC: WAG
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
WAG -1889.124 3788.249 - 0.00158 3788.503 - 0.0244 3805.694 + 0.568
WAG+I -1887.038 3786.075 - 0.0047 3786.433 + 0.0686 3807.009 + 0.294
WAG+G4 -1888.008 3788.016 - 0.00178 3788.374 - 0.026 3808.950 + 0.112
WAG+I+G4 -1887.097 3788.193 - 0.00163 3788.672 - 0.0224 3812.616 - 0.0178
WAG+R2 -1887.966 3789.933 - 0.000683 3790.411 - 0.00938 3814.355 - 0.00748
DCMut+I -1894.327 3800.654 - 3.21e-06 3801.012 - 4.68e-05 3821.588 - 0.000201
Dayhoff+I -1894.334 3800.668 - 3.18e-06 3801.026 - 4.65e-05 3821.602 - 0.0002
DCMut+G4 -1895.605 3803.210 - 8.93e-07 3803.568 - 1.3e-05 3824.144 - 5.6e-05
Dayhoff+G4 -1895.618 3803.235 - 8.82e-07 3803.593 - 1.29e-05 3824.169 - 5.53e-05
DCMut -1899.706 3809.412 - 4.02e-08 3809.667 - 6.18e-07 3826.857 - 1.44e-05
Dayhoff -1899.792 3809.584 - 3.69e-08 3809.838 - 5.67e-07 3827.028 - 1.32e-05
DCMut+I+G4 -1894.328 3802.656 - 1.18e-06 3803.134 - 1.62e-05 3827.078 - 1.29e-05
Dayhoff+I+G4 -1894.334 3802.669 - 1.17e-06 3803.147 - 1.61e-05 3827.091 - 1.28e-05
DCMut+R2 -1895.632 3805.264 - 3.2e-07 3805.743 - 4.4e-06 3829.686 - 3.5e-06
Dayhoff+R2 -1895.646 3805.292 - 3.15e-07 3805.770 - 4.34e-06 3829.714 - 3.46e-06
VT -1904.022 3818.045 - 5.37e-10 3818.299 - 8.25e-09 3835.489 - 1.92e-07
VT+I -1903.117 3818.235 - 4.88e-10 3818.592 - 7.13e-09 3839.168 - 3.06e-08
VT+G4 -1903.665 3819.330 - 2.82e-10 3819.688 - 4.12e-09 3840.264 - 1.77e-08
VT+I+G4 -1903.307 3820.614 - 1.49e-10 3821.092 - 2.04e-09 3845.036 - 1.63e-09
VT+R2 -1903.693 3821.387 - 1.01e-10 3821.865 - 1.39e-09 3845.809 - 1.11e-09
JTTDCMut+I -1910.360 3832.720 - 3.49e-13 3833.078 - 5.1e-12 3853.654 - 2.19e-11
Q.pfam+G4 -1910.474 3832.947 - 3.12e-13 3833.304 - 4.55e-12 3853.881 - 1.95e-11
JTTDCMut -1913.253 3836.505 - 5.26e-14 3836.759 - 8.09e-13 3853.950 - 1.89e-11
LG+G4 -1910.525 3833.049 - 2.96e-13 3833.406 - 4.33e-12 3853.983 - 1.86e-11
JTTDCMut+G4 -1910.765 3833.531 - 2.33e-13 3833.888 - 3.4e-12 3854.465 - 1.46e-11
LG+I -1910.795 3833.589 - 2.26e-13 3833.946 - 3.3e-12 3854.523 - 1.42e-11
Q.pfam+I -1910.889 3833.777 - 2.06e-13 3834.135 - 3.01e-12 3854.711 - 1.29e-11
JTT+I -1910.894 3833.788 - 2.05e-13 3834.145 - 2.99e-12 3854.722 - 1.28e-11
JTT -1913.764 3837.529 - 3.15e-14 3837.783 - 4.85e-13 3854.973 - 1.13e-11
JTT+G4 -1911.280 3834.561 - 1.39e-13 3834.918 - 2.03e-12 3855.495 - 8.72e-12
LG -1914.182 3838.364 - 2.08e-14 3838.619 - 3.19e-13 3855.809 - 7.45e-12
Q.pfam -1914.649 3839.298 - 1.3e-14 3839.553 - 2e-13 3856.743 - 4.67e-12
JTTDCMut+I+G4 -1910.387 3834.773 - 1.25e-13 3835.252 - 1.72e-12 3859.196 - 1.37e-12
Q.pfam+R2 -1910.534 3835.068 - 1.08e-13 3835.547 - 1.48e-12 3859.491 - 1.18e-12
Q.pfam+I+G4 -1910.595 3835.190 - 1.02e-13 3835.669 - 1.4e-12 3859.612 - 1.11e-12
LG+I+G4 -1910.603 3835.206 - 1.01e-13 3835.684 - 1.38e-12 3859.628 - 1.1e-12
LG+R2 -1910.609 3835.219 - 1e-13 3835.698 - 1.38e-12 3859.641 - 1.1e-12
JTTDCMut+R2 -1910.859 3835.717 - 7.8e-14 3836.196 - 1.07e-12 3860.140 - 8.54e-13
JTT+I+G4 -1910.920 3835.841 - 7.33e-14 3836.319 - 1.01e-12 3860.263 - 8.03e-13
JTT+R2 -1911.378 3836.756 - 4.64e-14 3837.235 - 6.38e-13 3861.179 - 5.08e-13
WAG+F -1865.503 3779.005 + 0.161 3784.535 + 0.177 3862.740 - 2.33e-13
WAG+F+I -1863.510 3777.021 + 0.434 3783.039 + 0.374 3864.244 - 1.1e-13
PMB -1918.652 3847.304 - 2.38e-16 3847.559 - 3.66e-15 3864.749 - 8.53e-14
LG+I+R2 -1910.426 3836.851 - 4.42e-14 3837.469 - 5.67e-13 3864.763 - 8.47e-14
WAG+F+G4 -1864.397 3778.795 + 0.179 3784.813 + 0.154 3866.018 - 4.52e-14
Blosum62 -1919.525 3849.049 - 9.93e-17 3849.303 - 1.53e-15 3866.494 - 3.56e-14
PMB+I -1917.874 3847.749 - 1.9e-16 3848.106 - 2.78e-15 3868.682 - 1.19e-14
PMB+G4 -1918.343 3848.686 - 1.19e-16 3849.043 - 1.74e-15 3869.619 - 7.47e-15
WAG+F+I+G4 -1863.587 3779.173 + 0.148 3785.704 + 0.0988 3869.886 - 6.54e-15
Blosum62+I -1918.590 3849.181 - 9.3e-17 3849.538 - 1.36e-15 3870.114 - 5.83e-15
LG+R3 -1910.514 3839.027 - 1.49e-14 3839.803 - 1.77e-13 3870.428 - 4.99e-15
Blosum62+G4 -1919.138 3850.276 - 5.38e-17 3850.634 - 7.86e-16 3871.210 - 3.37e-15
WAG+F+R2 -1864.382 3780.765 + 0.0668 3787.295 - 0.0446 3871.477 - 2.95e-15
PMB+I+G4 -1918.033 3850.066 - 5.98e-17 3850.545 - 8.21e-16 3874.488 - 6.54e-16
PMB+R2 -1918.366 3850.733 - 4.28e-17 3851.211 - 5.89e-16 3875.155 - 4.69e-16
LG+I+R3 -1910.379 3840.757 - 6.28e-15 3841.710 - 6.81e-14 3875.647 - 3.67e-16
Blosum62+I+G4 -1918.783 3851.567 - 2.82e-17 3852.045 - 3.88e-16 3875.989 - 3.09e-16
Blosum62+R2 -1919.144 3852.288 - 1.97e-17 3852.767 - 2.7e-16 3876.711 - 2.15e-16
VT+F -1873.107 3794.214 - 8.03e-05 3799.744 - 8.83e-05 3877.948 - 1.16e-16
VT+F+I -1872.110 3794.220 - 8e-05 3800.239 - 6.89e-05 3881.443 - 2.02e-17
VT+F+G4 -1872.668 3795.335 - 4.58e-05 3801.354 - 3.95e-05 3882.559 - 1.16e-17
DCMut+F+I -1873.793 3797.586 - 1.49e-05 3803.605 - 1.28e-05 3884.810 - 3.76e-18
Dayhoff+F+I -1873.837 3797.675 - 1.42e-05 3803.693 - 1.23e-05 3884.898 - 3.59e-18
Blosum62+F -1876.662 3801.323 - 2.29e-06 3806.853 - 2.52e-06 3885.058 - 3.32e-18
DCMut+F+G4 -1874.534 3799.069 - 7.08e-06 3805.087 - 6.1e-06 3886.292 - 1.79e-18
Dayhoff+F+G4 -1874.576 3799.152 - 6.8e-06 3805.170 - 5.85e-06 3886.375 - 1.72e-18
VT+F+I+G4 -1872.295 3796.590 - 2.45e-05 3803.120 - 1.63e-05 3887.302 - 1.08e-18
PMB+F -1877.832 3803.663 - 7.12e-07 3809.193 - 7.83e-07 3887.398 - 1.03e-18
VT+F+R2 -1872.733 3797.465 - 1.58e-05 3803.996 - 1.05e-05 3888.178 - 6.97e-19
Blosum62+F+I -1875.720 3801.439 - 2.17e-06 3807.458 - 1.87e-06 3888.663 - 5.47e-19
Blosum62+F+G4 -1876.219 3802.439 - 1.31e-06 3808.457 - 1.13e-06 3889.662 - 3.32e-19
LG+F+G4 -1876.385 3802.771 - 1.11e-06 3808.789 - 9.59e-07 3889.994 - 2.81e-19
DCMut+F+I+G4 -1873.723 3799.446 - 5.86e-06 3805.976 - 3.91e-06 3890.159 - 2.59e-19
Dayhoff+F+I+G4 -1873.761 3799.521 - 5.65e-06 3806.052 - 3.77e-06 3890.234 - 2.49e-19
DCMut+F -1879.322 3806.644 - 1.6e-07 3812.174 - 1.76e-07 3890.379 - 2.32e-19
Dayhoff+F -1879.446 3806.893 - 1.42e-07 3812.423 - 1.56e-07 3890.627 - 2.05e-19
LG+F+I -1876.868 3803.736 - 6.87e-07 3809.755 - 5.91e-07 3890.960 - 1.73e-19
PMB+F+I -1877.064 3804.127 - 5.65e-07 3810.146 - 4.87e-07 3891.350 - 1.43e-19
DCMut+F+R2 -1874.674 3801.349 - 2.27e-06 3807.879 - 1.51e-06 3892.061 - 1e-19
Dayhoff+F+R2 -1874.719 3801.438 - 2.17e-06 3807.968 - 1.45e-06 3892.150 - 9.56e-20
PMB+F+G4 -1877.521 3805.041 - 3.58e-07 3811.060 - 3.08e-07 3892.265 - 9.03e-20
LG+F -1880.399 3808.797 - 5.47e-08 3814.327 - 6.01e-08 3892.532 - 7.9e-20
Q.pfam+F+G4 -1877.813 3805.626 - 2.67e-07 3811.645 - 2.3e-07 3892.850 - 6.74e-20
Q.pfam+F+I -1878.403 3806.806 - 1.48e-07 3812.825 - 1.27e-07 3894.030 - 3.74e-20
Blosum62+F+I+G4 -1875.859 3803.718 - 6.93e-07 3810.249 - 4.62e-07 3894.431 - 3.06e-20
Blosum62+F+R2 -1876.271 3804.543 - 4.59e-07 3811.073 - 3.06e-07 3895.255 - 2.03e-20
Q.pfam+F -1881.905 3811.811 - 1.21e-08 3817.341 - 1.33e-08 3895.545 - 1.75e-20
LG+F+R2 -1876.537 3805.074 - 3.52e-07 3811.605 - 2.35e-07 3895.787 - 1.55e-20
LG+F+I+G4 -1876.589 3805.178 - 3.34e-07 3811.708 - 2.23e-07 3895.890 - 1.47e-20
PMB+F+I+G4 -1877.228 3806.455 - 1.76e-07 3812.985 - 1.18e-07 3897.167 - 7.78e-21
PMB+F+R2 -1877.554 3807.107 - 1.27e-07 3813.637 - 8.49e-08 3897.819 - 5.62e-21
Q.pfam+F+R2 -1877.948 3807.895 - 8.58e-08 3814.425 - 5.72e-08 3898.608 - 3.79e-21
Q.pfam+F+I+G4 -1878.088 3808.176 - 7.46e-08 3814.706 - 4.98e-08 3898.888 - 3.29e-21
JTTDCMut+F+G4 -1883.592 3817.183 - 8.25e-10 3823.202 - 7.11e-10 3904.407 - 2.09e-22
JTTDCMut+F+I -1883.593 3817.186 - 8.24e-10 3823.204 - 7.1e-10 3904.409 - 2.08e-22
JTT+F+I -1883.788 3817.576 - 6.78e-10 3823.595 - 5.84e-10 3904.800 - 1.71e-22
JTT+F+G4 -1883.790 3817.579 - 6.77e-10 3823.598 - 5.83e-10 3904.802 - 1.71e-22
JTTDCMut+F -1886.925 3821.851 - 8e-11 3827.381 - 8.8e-11 3905.585 - 1.16e-22
JTT+F -1887.137 3822.273 - 6.48e-11 3827.803 - 7.13e-11 3906.008 - 9.37e-23
JTTDCMut+F+I+G4 -1883.515 3819.031 - 3.28e-10 3825.561 - 2.19e-10 3909.743 - 1.45e-23
JTT+F+I+G4 -1883.708 3819.415 - 2.7e-10 3825.945 - 1.8e-10 3910.128 - 1.19e-23
JTTDCMut+F+R2 -1883.798 3819.595 - 2.47e-10 3826.126 - 1.65e-10 3910.308 - 1.09e-23
JTT+F+R2 -1884.000 3820.000 - 2.02e-10 3826.531 - 1.35e-10 3910.713 - 8.91e-24
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: WAG
State frequencies: (model)
Model of rate heterogeneity: Uniform
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -1889.1243 (s.e. 43.0816)
Unconstrained log-likelihood (without tree): -1228.7131
Number of free parameters (#branches + #model parameters): 5
Akaike information criterion (AIC) score: 3788.2486
Corrected Akaike information criterion (AICc) score: 3788.5028
Bayesian information criterion (BIC) score: 3805.6933
Total tree length (sum of branch lengths): 1.6536
Sum of internal branch lengths: 0.5114 (30.9252% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'PYAP_22273' is drawn at root
+-------PYAP_22273
|
+---------PYAR_24096
|
| +-------------------------------PYIW_18788
+--------------------------|
+---------PYU1_G001739
Tree in newick format:
(PYAP_22273:0.1518991454,PYAR_24096:0.1921751589,(PYIW_18788:0.6101885954,PYU1_G001739:0.1879670795):0.5113836347);
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 "WAG" --length 242
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: Sat Apr 20 14:20:59 2024
Total CPU time used: 0.798202 seconds (0h:0m:0s)
Total wall-clock time used: 0.313163 seconds (0h:0m:0s)