(PHALS_12600:0.9290562021,PHYRA_81102:0.0940838528,(PHYCA_129485:0.0774060215,(PITG_18453:0.0773951437,PPTG_17125:0.0291521288):0.0473037781):0.0838761072);
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: 135681
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: 5 sequences with 251 amino-acid sites
Number of constant sites: 88 (= 35.0598% of all sites)
Number of invariant (constant or ambiguous constant) sites: 88 (= 35.0598% of all sites)
Number of parsimony informative sites: 22
Number of distinct site patterns: 169
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 -1735.360 3484.719 + 0.18 3485.180 + 0.193 3509.397 + 0.623
WAG+G4 -1733.420 3482.840 + 0.459 3483.435 + 0.461 3511.044 + 0.274
WAG+I -1734.717 3485.434 + 0.126 3486.029 + 0.126 3513.638 + 0.0748
WAG+R2 -1733.472 3484.944 + 0.16 3485.691 + 0.149 3516.673 - 0.0164
WAG+I+G4 -1734.353 3486.707 + 0.0665 3487.454 + 0.0619 3518.436 - 0.00679
JTTDCMut+G4 -1738.394 3492.788 - 0.00318 3493.383 - 0.00319 3520.992 - 0.00189
VT -1742.037 3498.075 - 0.000226 3498.536 - 0.000243 3522.753 - 0.000784
JTT+G4 -1739.406 3494.812 - 0.00115 3495.408 - 0.00116 3523.016 - 0.000688
JTTDCMut -1742.262 3498.525 - 0.00018 3498.986 - 0.000194 3523.203 - 0.000626
JTTDCMut+I -1740.342 3496.685 - 0.000453 3497.280 - 0.000455 3524.888 - 0.00027
JTT -1743.369 3500.738 - 5.97e-05 3501.199 - 6.41e-05 3525.417 - 0.000207
VT+G4 -1740.659 3497.318 - 0.00033 3497.913 - 0.000331 3525.521 - 0.000197
JTTDCMut+R2 -1738.406 3494.812 - 0.00116 3495.559 - 0.00108 3526.541 - 0.000118
JTT+I -1741.425 3498.851 - 0.000153 3499.446 - 0.000154 3527.054 - 9.13e-05
VT+I -1741.658 3499.317 - 0.000121 3499.912 - 0.000122 3527.520 - 7.23e-05
Q.pfam+G4 -1741.889 3499.778 - 9.64e-05 3500.373 - 9.68e-05 3527.982 - 5.74e-05
JTTDCMut+I+G4 -1739.279 3496.557 - 0.000483 3497.304 - 0.000449 3528.286 - 4.93e-05
JTT+R2 -1739.413 3496.825 - 0.000422 3497.572 - 0.000393 3528.554 - 4.31e-05
JTT+I+G4 -1740.302 3498.605 - 0.000173 3499.352 - 0.000161 3530.334 - 1.77e-05
VT+R2 -1740.720 3499.441 - 0.000114 3500.188 - 0.000106 3531.170 - 1.17e-05
LG+G4 -1743.542 3503.083 - 1.85e-05 3503.678 - 1.86e-05 3531.287 - 1.1e-05
Q.pfam -1747.011 3508.022 - 1.56e-06 3508.483 - 1.68e-06 3532.701 - 5.43e-06
VT+I+G4 -1741.678 3501.357 - 4.38e-05 3502.104 - 4.08e-05 3533.086 - 4.48e-06
Q.pfam+R2 -1741.829 3501.659 - 3.77e-05 3502.405 - 3.51e-05 3533.388 - 3.85e-06
Q.pfam+I -1745.257 3506.513 - 3.32e-06 3507.108 - 3.34e-06 3534.717 - 1.98e-06
Q.pfam+I+G4 -1742.836 3503.671 - 1.38e-05 3504.418 - 1.28e-05 3535.400 - 1.41e-06
LG+R2 -1743.529 3505.058 - 6.88e-06 3505.805 - 6.41e-06 3536.787 - 7.03e-07
LG -1749.272 3512.544 - 1.63e-07 3513.004 - 1.75e-07 3537.222 - 5.66e-07
LG+I -1746.995 3509.990 - 5.85e-07 3510.585 - 5.87e-07 3538.193 - 3.48e-07
LG+I+G4 -1744.519 3507.038 - 2.56e-06 3507.785 - 2.38e-06 3538.767 - 2.61e-07
LG+I+R2 -1743.349 3506.697 - 3.03e-06 3507.614 - 2.59e-06 3541.952 - 5.32e-08
PMB -1753.511 3521.022 - 2.35e-09 3521.483 - 2.52e-09 3545.700 - 8.16e-09
DCMut+G4 -1750.784 3517.567 - 1.32e-08 3518.162 - 1.33e-08 3545.771 - 7.88e-09
Dayhoff+G4 -1750.785 3517.569 - 1.32e-08 3518.164 - 1.33e-08 3545.773 - 7.87e-09
Blosum62 -1753.575 3521.150 - 2.21e-09 3521.611 - 2.37e-09 3545.828 - 7.65e-09
LG+R3 -1742.582 3507.164 - 2.4e-06 3508.269 - 1.87e-06 3545.944 - 7.22e-09
Blosum62+G4 -1752.135 3520.271 - 3.42e-09 3520.866 - 3.44e-09 3548.474 - 2.04e-09
DCMut -1755.021 3524.041 - 5.2e-10 3524.502 - 5.58e-10 3548.719 - 1.8e-09
Dayhoff -1755.081 3524.162 - 4.89e-10 3524.623 - 5.25e-10 3548.841 - 1.7e-09
PMB+G4 -1752.567 3521.134 - 2.22e-09 3521.729 - 2.23e-09 3549.337 - 1.32e-09
DCMut+I -1753.197 3522.394 - 1.18e-09 3522.989 - 1.19e-09 3550.598 - 7.05e-10
Blosum62+I -1753.204 3522.408 - 1.18e-09 3523.003 - 1.18e-09 3550.612 - 7e-10
Dayhoff+I -1753.225 3522.449 - 1.15e-09 3523.044 - 1.16e-09 3550.653 - 6.86e-10
PMB+I -1753.369 3522.738 - 9.97e-10 3523.333 - 1e-09 3550.941 - 5.94e-10
Dayhoff+R2 -1750.840 3519.679 - 4.6e-09 3520.426 - 4.28e-09 3551.408 - 4.7e-10
DCMut+R2 -1750.840 3519.680 - 4.6e-09 3520.427 - 4.28e-09 3551.409 - 4.7e-10
LG+I+R3 -1742.602 3509.203 - 8.66e-07 3510.514 - 6.08e-07 3551.509 - 4.47e-10
DCMut+I+G4 -1751.686 3521.372 - 1.97e-09 3522.119 - 1.84e-09 3553.101 - 2.02e-10
Dayhoff+I+G4 -1751.686 3521.373 - 1.97e-09 3522.120 - 1.84e-09 3553.102 - 2.02e-10
Blosum62+R2 -1752.190 3522.380 - 1.19e-09 3523.127 - 1.11e-09 3554.109 - 1.22e-10
PMB+R2 -1752.632 3523.265 - 7.66e-10 3524.012 - 7.13e-10 3554.994 - 7.83e-11
Blosum62+I+G4 -1753.107 3524.214 - 4.76e-10 3524.961 - 4.43e-10 3555.944 - 4.87e-11
PMB+I+G4 -1753.571 3525.143 - 3e-10 3525.889 - 2.79e-10 3556.872 - 3.06e-11
WAG+F -1729.425 3510.850 - 3.8e-07 3517.118 - 2.24e-08 3602.512 - 3.76e-21
WAG+F+G4 -1727.684 3509.368 - 7.98e-07 3516.148 - 3.64e-08 3604.555 - 1.35e-21
WAG+F+I -1728.871 3511.743 - 2.43e-07 3518.523 - 1.11e-08 3606.930 - 4.13e-22
JTTDCMut+F+G4 -1729.627 3513.254 - 1.14e-07 3520.034 - 5.21e-09 3608.441 - 1.94e-22
JTT+F+G4 -1730.459 3514.918 - 4.97e-08 3521.699 - 2.27e-09 3610.106 - 8.44e-23
WAG+F+R2 -1727.740 3511.480 - 2.77e-07 3518.795 - 9.68e-09 3610.193 - 8.08e-23
JTTDCMut+F -1733.292 3518.585 - 7.95e-09 3524.852 - 4.68e-10 3610.246 - 7.86e-23
WAG+F+I+G4 -1728.611 3513.223 - 1.16e-07 3520.538 - 4.05e-09 3611.935 - 3.38e-23
JTT+F -1734.215 3520.431 - 3.16e-09 3526.699 - 1.86e-10 3612.093 - 3.12e-23
JTTDCMut+F+I -1731.497 3516.993 - 1.76e-08 3523.773 - 8.03e-10 3612.180 - 2.99e-23
Dayhoff+F+G4 -1731.941 3517.881 - 1.13e-08 3524.661 - 5.15e-10 3613.068 - 1.92e-23
DCMut+F+G4 -1731.952 3517.904 - 1.12e-08 3524.684 - 5.09e-10 3613.091 - 1.9e-23
JTT+F+I -1732.384 3518.769 - 7.25e-09 3525.549 - 3.31e-10 3613.956 - 1.23e-23
JTTDCMut+F+R2 -1729.646 3515.292 - 4.12e-08 3522.608 - 1.44e-09 3614.005 - 1.2e-23
VT+F -1735.228 3522.455 - 1.15e-09 3528.723 - 6.76e-11 3614.117 - 1.14e-23
DCMut+F -1735.652 3523.304 - 7.51e-10 3529.572 - 4.42e-11 3614.966 - 7.43e-24
Dayhoff+F -1735.693 3523.386 - 7.21e-10 3529.653 - 4.25e-11 3615.047 - 7.13e-24
JTT+F+R2 -1730.476 3516.952 - 1.8e-08 3524.267 - 6.27e-10 3615.665 - 5.24e-24
JTTDCMut+F+I+G4 -1730.511 3517.023 - 1.74e-08 3524.338 - 6.06e-10 3615.736 - 5.05e-24
VT+F+G4 -1734.030 3522.060 - 1.4e-09 3528.841 - 6.38e-11 3617.248 - 2.37e-24
JTT+F+I+G4 -1731.351 3518.702 - 7.5e-09 3526.017 - 2.62e-10 3617.414 - 2.18e-24
DCMut+F+I -1734.255 3522.511 - 1.12e-09 3529.291 - 5.09e-11 3617.698 - 1.89e-24
Dayhoff+F+I -1734.270 3522.539 - 1.1e-09 3529.320 - 5.02e-11 3617.727 - 1.87e-24
Dayhoff+F+R2 -1731.969 3519.938 - 4.04e-09 3527.254 - 1.41e-10 3618.651 - 1.18e-24
DCMut+F+R2 -1731.983 3519.966 - 3.99e-09 3527.281 - 1.39e-10 3618.679 - 1.16e-24
LG+F+G4 -1734.872 3523.745 - 6.03e-10 3530.525 - 2.75e-11 3618.932 - 1.02e-24
VT+F+I -1734.902 3523.804 - 5.85e-10 3530.585 - 2.67e-11 3618.992 - 9.92e-25
Q.pfam+F+G4 -1735.367 3524.735 - 3.67e-10 3531.515 - 1.67e-11 3619.922 - 6.23e-25
Dayhoff+F+I+G4 -1732.799 3521.599 - 1.76e-09 3528.914 - 6.14e-11 3620.312 - 5.13e-25
DCMut+F+I+G4 -1732.811 3521.623 - 1.74e-09 3528.938 - 6.07e-11 3620.336 - 5.07e-25
VT+F+R2 -1734.096 3524.193 - 4.82e-10 3531.508 - 1.68e-11 3622.905 - 1.4e-25
Q.pfam+F -1740.067 3532.134 - 9.08e-12 3538.402 - 5.35e-13 3623.795 - 8.98e-26
LG+F -1740.117 3532.234 - 8.64e-12 3538.502 - 5.09e-13 3623.896 - 8.54e-26
LG+F+R2 -1734.934 3525.869 - 2.08e-10 3533.184 - 7.27e-12 3624.581 - 6.06e-26
VT+F+I+G4 -1735.024 3526.049 - 1.9e-10 3533.364 - 6.64e-12 3624.762 - 5.54e-26
LG+F+I -1737.952 3529.903 - 2.77e-11 3536.684 - 1.26e-12 3625.090 - 4.7e-26
Q.pfam+F+R2 -1735.368 3526.737 - 1.35e-10 3534.052 - 4.71e-12 3625.449 - 3.93e-26
Q.pfam+F+I -1738.382 3530.764 - 1.8e-11 3537.544 - 8.21e-13 3625.951 - 3.06e-26
LG+F+I+G4 -1735.823 3527.646 - 8.56e-11 3534.962 - 2.99e-12 3626.359 - 2.49e-26
Blosum62+F -1741.479 3534.959 - 2.21e-12 3541.226 - 1.3e-13 3626.620 - 2.19e-26
Q.pfam+F+I+G4 -1736.293 3528.586 - 5.35e-11 3535.901 - 1.87e-12 3627.298 - 1.56e-26
PMB+F -1742.225 3536.450 - 1.05e-12 3542.718 - 6.18e-14 3628.112 - 1.04e-26
Blosum62+F+G4 -1740.168 3534.336 - 3.02e-12 3541.116 - 1.38e-13 3629.523 - 5.13e-27
Blosum62+F+I -1741.097 3536.193 - 1.19e-12 3542.973 - 5.44e-14 3631.380 - 2.02e-27
PMB+F+G4 -1741.315 3536.630 - 9.59e-13 3543.411 - 4.37e-14 3631.818 - 1.63e-27
PMB+F+I -1742.076 3538.152 - 4.48e-13 3544.933 - 2.04e-14 3633.340 - 7.6e-28
Blosum62+F+R2 -1740.232 3536.465 - 1.04e-12 3543.780 - 3.63e-14 3635.177 - 3.03e-28
Blosum62+F+I+G4 -1741.167 3538.335 - 4.09e-13 3545.650 - 1.43e-14 3637.047 - 1.19e-28
PMB+F+R2 -1741.386 3538.772 - 3.29e-13 3546.088 - 1.15e-14 3637.485 - 9.57e-29
PMB+F+I+G4 -1742.296 3540.591 - 1.32e-13 3547.906 - 4.62e-15 3639.304 - 3.85e-29
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: -1735.3595 (s.e. 50.6494)
Unconstrained log-likelihood (without tree): -1226.3579
Number of free parameters (#branches + #model parameters): 7
Akaike information criterion (AIC) score: 3484.7190
Corrected Akaike information criterion (AICc) score: 3485.1799
Bayesian information criterion (BIC) score: 3509.3971
Total tree length (sum of branch lengths): 1.3383
Sum of internal branch lengths: 0.1312 (9.8022% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'PHALS_12600' is drawn at root
+-----------------------------------------------------------PHALS_12600
|
+-----PHYRA_81102
|
| +---PHYCA_129485
+----|
| +---PITG_18453
+--|
+--PPTG_17125
Tree in newick format:
(PHALS_12600:0.9290562021,PHYRA_81102:0.0940838528,(PHYCA_129485:0.0774060215,(PITG_18453:0.0773951437,PPTG_17125:0.0291521288):0.0473037781):0.0838761072);
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 251
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 07:08:10 2024
Total CPU time used: 1.40105 seconds (0h:0m:1s)
Total wall-clock time used: 0.508097 seconds (0h:0m:0s)