(PYVX_15869:1.0134592612,((((PHALS_10836:0.8293731219,(PITG_00012:0.0513089591,PPTG_16671:0.0334785439):0.0184105923):0.0446073151,PHYCA_104436:0.1027244955):0.0645485748,PHYSO_554653:0.2246280280):0.0300977024,PHYRA_78819:0.1272354642):0.1222879027,HYAP_01509:0.3837166417);
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: 818618
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: 8 sequences with 209 amino-acid sites
Number of constant sites: 40 (= 19.1388% of all sites)
Number of invariant (constant or ambiguous constant) sites: 40 (= 19.1388% of all sites)
Number of parsimony informative sites: 46
Number of distinct site patterns: 185
ModelFinder
-----------
Best-fit model according to BIC: JTT+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
JTT+G4 -2305.719 4639.439 - 2.45e-06 4641.604 - 0.00063 4686.231 + 0.517
JTTDCMut+G4 -2306.465 4640.929 - 1.16e-06 4643.094 - 0.000299 4687.722 + 0.245
JTT+R2 -2304.454 4638.909 - 3.19e-06 4641.396 - 0.000698 4689.044 + 0.127
JTTDCMut+R2 -2305.279 4640.558 - 1.4e-06 4643.045 - 0.000306 4690.693 + 0.0555
JTT+I+G4 -2306.087 4642.174 - 6.24e-07 4644.661 - 0.000137 4692.309 - 0.0247
JTT+I+R2 -2304.035 4640.069 - 1.79e-06 4642.903 - 0.000329 4693.547 - 0.0133
JTTDCMut+I+G4 -2306.811 4643.621 - 3.03e-07 4646.108 - 6.62e-05 4693.756 - 0.012
JTTDCMut+I+R2 -2304.824 4641.648 - 8.12e-07 4644.481 - 0.000149 4695.125 - 0.00605
VT+G4 -2321.154 4670.308 - 4.85e-13 4672.473 - 1.25e-10 4717.100 - 1.02e-07
VT+R2 -2319.792 4669.584 - 6.97e-13 4672.071 - 1.52e-10 4719.719 - 2.76e-08
WAG+G4 -2322.985 4673.969 - 7.78e-14 4676.134 - 2e-11 4720.762 - 1.64e-08
VT+I+G4 -2321.627 4673.254 - 1.11e-13 4675.741 - 2.43e-11 4723.389 - 4.41e-09
WAG+R2 -2322.135 4674.269 - 6.7e-14 4676.756 - 1.46e-11 4724.404 - 2.65e-09
VT+I+R2 -2319.648 4671.295 - 2.96e-13 4674.129 - 5.45e-11 4724.773 - 2.21e-09
JTTDCMut+F+G4 -2274.963 4615.925 + 0.313 4628.748 + 0.39 4726.222 - 1.07e-09
WAG+I+G4 -2323.362 4676.723 - 1.96e-14 4679.210 - 4.29e-12 4726.858 - 7.78e-10
JTT+F+G4 -2275.458 4616.915 + 0.191 4629.738 + 0.237 4727.212 - 6.52e-10
WAG+I+R2 -2321.676 4675.352 - 3.9e-14 4678.185 - 7.17e-12 4728.829 - 2.9e-10
Q.pfam+G4 -2327.934 4683.867 - 5.52e-16 4686.032 - 1.42e-13 4730.660 - 1.16e-10
JTTDCMut+F+R2 -2274.837 4617.673 + 0.13 4631.351 + 0.106 4731.312 - 8.39e-11
JTTDCMut+F+I+G4 -2275.085 4618.170 + 0.102 4631.848 + 0.0827 4731.809 - 6.55e-11
JTT+F+R2 -2275.313 4618.627 + 0.081 4632.305 + 0.0658 4732.266 - 5.21e-11
Q.pfam+R2 -2326.278 4682.557 - 1.06e-15 4685.044 - 2.32e-13 4732.692 - 4.21e-11
JTT+F+I+G4 -2275.576 4619.153 + 0.0622 4632.831 + 0.0506 4732.792 - 4e-11
JTTDCMut+F+I+R2 -2274.424 4618.849 + 0.0725 4633.415 - 0.0378 4735.830 - 8.77e-12
WAG+F+G4 -2279.951 4625.902 - 0.00213 4638.725 - 0.00266 4736.199 - 7.29e-12
JTT+F+I+R2 -2274.897 4619.793 - 0.0452 4634.360 - 0.0236 4736.775 - 5.47e-12
Q.pfam+I+G4 -2328.435 4686.869 - 1.23e-16 4689.356 - 2.69e-14 4737.004 - 4.88e-12
Q.pfam+I+R2 -2325.972 4683.944 - 5.31e-16 4686.778 - 9.76e-14 4737.422 - 3.96e-12
WAG+F+R2 -2280.095 4628.190 - 0.000679 4641.868 - 0.000552 4741.829 - 4.37e-13
WAG+F+I+G4 -2280.273 4628.545 - 0.000568 4642.223 - 0.000462 4742.184 - 3.66e-13
VT+F+G4 -2284.351 4634.701 - 2.62e-05 4647.524 - 3.26e-05 4744.998 - 8.96e-14
WAG+F+I+R2 -2279.682 4629.365 - 0.000377 4643.931 - 0.000197 4746.347 - 4.56e-14
LG+G4 -2335.794 4699.588 - 2.13e-19 4701.753 - 5.47e-17 4746.381 - 4.49e-14
Q.pfam+F+G4 -2285.659 4637.317 - 7.08e-06 4650.140 - 8.82e-06 4747.614 - 2.42e-14
LG+F+G4 -2286.004 4638.008 - 5.01e-06 4650.831 - 6.24e-06 4748.305 - 1.71e-14
LG+R2 -2334.368 4698.736 - 3.26e-19 4701.223 - 7.13e-17 4748.871 - 1.29e-14
VT+F+R2 -2283.910 4635.821 - 1.5e-05 4649.499 - 1.22e-05 4749.460 - 9.62e-15
VT+F+I+G4 -2284.794 4637.587 - 6.18e-06 4651.265 - 5.02e-06 4751.227 - 3.98e-15
Q.pfam+F+R2 -2285.136 4638.272 - 4.39e-06 4651.950 - 3.57e-06 4751.912 - 2.82e-15
LG+I+G4 -2336.225 4702.450 - 5.09e-20 4704.937 - 1.11e-17 4752.585 - 2.02e-15
LG+I+R2 -2333.720 4699.439 - 2.29e-19 4702.272 - 4.22e-17 4752.916 - 1.71e-15
LG+F+R2 -2285.756 4639.511 - 2.36e-06 4653.189 - 1.92e-06 4753.150 - 1.52e-15
Q.pfam+F+I+G4 -2286.151 4640.303 - 1.59e-06 4653.981 - 1.29e-06 4753.942 - 1.02e-15
LG+F+I+G4 -2286.402 4640.805 - 1.24e-06 4654.483 - 1.01e-06 4754.444 - 7.96e-16
VT+F+I+R2 -2283.760 4637.520 - 6.39e-06 4652.086 - 3.33e-06 4754.501 - 7.74e-16
Q.pfam+F+I+R2 -2284.815 4639.630 - 2.23e-06 4654.196 - 1.16e-06 4756.611 - 2.69e-16
LG+F+I+R2 -2285.344 4640.689 - 1.31e-06 4655.255 - 6.83e-07 4757.671 - 1.59e-16
LG+R3 -2334.461 4702.922 - 4.02e-20 4706.126 - 6.14e-18 4759.742 - 5.63e-17
PMB+G4 -2342.505 4713.011 - 2.59e-22 4715.176 - 6.65e-20 4759.804 - 5.46e-17
PMB+R2 -2341.206 4712.412 - 3.49e-22 4714.899 - 7.64e-20 4762.547 - 1.38e-17
LG+I+R3 -2333.760 4703.521 - 2.98e-20 4707.121 - 3.73e-18 4763.683 - 7.85e-18
PMB+I+G4 -2342.942 4715.883 - 6.16e-23 4718.371 - 1.35e-20 4766.018 - 2.44e-18
PMB+I+R2 -2340.903 4713.805 - 1.74e-22 4716.639 - 3.2e-20 4767.283 - 1.3e-18
LG+I -2349.178 4726.356 - 3.28e-25 4728.521 - 8.42e-23 4773.149 - 6.91e-20
PMB+F+G4 -2303.986 4673.972 - 7.77e-14 4686.795 - 9.68e-14 4784.269 - 2.66e-22
Blosum62+G4 -2355.776 4739.551 - 4.47e-28 4741.716 - 1.15e-25 4786.344 - 9.42e-23
Blosum62+F+G4 -2305.367 4676.735 - 1.95e-14 4689.557 - 2.43e-14 4787.032 - 6.68e-23
Dayhoff+F+G4 -2305.516 4677.031 - 1.68e-14 4689.854 - 2.1e-14 4787.328 - 5.76e-23
DCMut+F+G4 -2305.538 4677.077 - 1.64e-14 4689.900 - 2.05e-14 4787.374 - 5.63e-23
PMB+F+R2 -2303.116 4674.233 - 6.82e-14 4687.911 - 5.54e-14 4787.872 - 4.39e-23
Blosum62+R2 -2353.875 4737.751 - 1.1e-27 4740.238 - 2.4e-25 4787.886 - 4.36e-23
Dayhoff+G4 -2357.364 4742.728 - 9.12e-29 4744.893 - 2.34e-26 4789.521 - 1.92e-23
DCMut+G4 -2357.392 4742.783 - 8.87e-29 4744.948 - 2.28e-26 4789.576 - 1.87e-23
Blosum62+F+R2 -2304.057 4676.113 - 2.66e-14 4689.791 - 2.16e-14 4789.752 - 1.71e-23
PMB+F+I+G4 -2304.521 4677.041 - 1.67e-14 4690.719 - 1.36e-14 4790.681 - 1.08e-23
Blosum62+I+G4 -2356.253 4742.506 - 1.02e-28 4744.993 - 2.23e-26 4792.641 - 4.04e-24
Blosum62+I+R2 -2353.620 4739.240 - 5.22e-28 4742.073 - 9.6e-26 4792.717 - 3.89e-24
PMB+F+I+R2 -2302.971 4675.941 - 2.9e-14 4690.508 - 1.51e-14 4792.923 - 3.51e-24
Dayhoff+F+R2 -2305.697 4679.395 - 5.16e-15 4693.073 - 4.19e-15 4793.034 - 3.32e-24
DCMut+F+R2 -2305.708 4679.417 - 5.1e-15 4693.095 - 4.15e-15 4793.056 - 3.28e-24
Dayhoff+R2 -2356.465 4742.930 - 8.24e-29 4745.417 - 1.8e-26 4793.065 - 3.27e-24
DCMut+R2 -2356.486 4742.972 - 8.07e-29 4745.459 - 1.77e-26 4793.107 - 3.2e-24
Dayhoff+F+I+G4 -2305.833 4679.667 - 4.5e-15 4693.345 - 3.66e-15 4793.306 - 2.9e-24
DCMut+F+I+G4 -2305.856 4679.711 - 4.41e-15 4693.389 - 3.58e-15 4793.350 - 2.83e-24
Blosum62+F+I+G4 -2305.919 4679.838 - 4.13e-15 4693.516 - 3.36e-15 4793.477 - 2.66e-24
LG -2362.634 4751.268 - 1.28e-30 4753.135 - 3.8e-28 4794.719 - 1.43e-24
Blosum62+F+I+R2 -2304.009 4678.017 - 1.03e-14 4692.584 - 5.36e-15 4794.999 - 1.24e-24
Dayhoff+I+G4 -2357.699 4745.399 - 2.4e-29 4747.886 - 5.25e-27 4795.534 - 9.52e-25
DCMut+I+G4 -2357.727 4745.454 - 2.33e-29 4747.941 - 5.11e-27 4795.589 - 9.26e-25
Dayhoff+I+R2 -2355.057 4742.113 - 1.24e-28 4744.947 - 2.28e-26 4795.591 - 9.25e-25
DCMut+I+R2 -2355.091 4742.183 - 1.2e-28 4745.016 - 2.2e-26 4795.660 - 8.93e-25
Dayhoff+F+I+R2 -2304.663 4679.326 - 5.34e-15 4693.892 - 2.78e-15 4796.307 - 6.46e-25
DCMut+F+I+R2 -2304.686 4679.372 - 5.22e-15 4693.938 - 2.72e-15 4796.353 - 6.32e-25
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+G4
State frequencies: (model)
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 1.6213
Category Relative_rate Proportion
1 0.2435 0.2500
2 0.6076 0.2500
3 1.0568 0.2500
4 2.0922 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: -2305.0663 (s.e. 69.7087)
Unconstrained log-likelihood (without tree): -1068.3273
Number of free parameters (#branches + #model parameters): 14
Akaike information criterion (AIC) score: 4638.1327
Corrected Akaike information criterion (AICc) score: 4640.2976
Bayesian information criterion (BIC) score: 4684.9254
Total tree length (sum of branch lengths): 3.0459
Sum of internal branch lengths: 0.2800 (9.1912% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'PYVX_15869' is drawn at root
+------------------------------------------------------PYVX_15869
|
| +--------------------------------------------PHALS_10836
| +--|
| | | +--PITG_00012
| | +--|
| | +--PPTG_16671
| +--|
| | +----PHYCA_104436
| +--|
| | +-----------PHYSO_554653
+-----|
| +-----PHYRA_78819
|
+--------------------HYAP_01509
Tree in newick format:
(PYVX_15869:1.0134592612,((((PHALS_10836:0.8293731219,(PITG_00012:0.0513089591,PPTG_16671:0.0334785439):0.0184105923):0.0446073151,PHYCA_104436:0.1027244955):0.0645485748,PHYSO_554653:0.2246280280):0.0300977024,PHYRA_78819:0.1272354642):0.1222879027,HYAP_01509:0.3837166417);
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+G4{1.62127}" --length 209
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: Wed Apr 24 09:21:14 2024
Total CPU time used: 10.9056 seconds (0h:0m:10s)
Total wall-clock time used: 3.718 seconds (0h:0m:3s)