(PYVX_18179:0.9150576917,((((PHALS_06480:0.8688068739,PHYKE_8390:0.0639669619):0.0894000711,PHYRA_81105:0.0475645034):0.0511657606,PHYSO_353401:0.0428087006):0.1235969409,HYAP_07096:0.2198359657):0.2196321656,PYU1_G001738:0.4800691378);
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: 316787
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: 7 sequences with 158 amino-acid sites
Number of constant sites: 31 (= 19.6203% of all sites)
Number of invariant (constant or ambiguous constant) sites: 31 (= 19.6203% of all sites)
Number of parsimony informative sites: 33
Number of distinct site patterns: 154
ModelFinder
-----------
Best-fit model according to BIC: WAG+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
WAG+G4 -1556.418 3136.837 + 0.404 3138.989 + 0.449 3173.588 + 0.681
WAG+I -1557.853 3139.706 + 0.0962 3141.858 + 0.107 3176.458 + 0.162
WAG+R2 -1555.901 3137.801 + 0.249 3140.329 + 0.229 3177.615 + 0.0909
WAG+I+G4 -1556.334 3138.668 + 0.162 3141.196 + 0.149 3178.482 + 0.0589
WAG+I+R2 -1555.940 3139.879 + 0.0883 3142.816 + 0.0662 3182.755 - 0.00696
Q.pfam+G4 -1564.788 3153.575 - 9.37e-05 3155.727 - 0.000104 3190.327 - 0.000158
JTTDCMut+G4 -1566.482 3156.964 - 1.72e-05 3159.116 - 1.91e-05 3193.715 - 2.9e-05
LG+G4 -1566.593 3157.185 - 1.54e-05 3159.337 - 1.71e-05 3193.936 - 2.6e-05
Q.pfam+R2 -1564.400 3154.800 - 5.08e-05 3157.328 - 4.67e-05 3194.614 - 1.85e-05
JTT+G4 -1567.026 3158.052 - 9.99e-06 3160.203 - 1.11e-05 3194.803 - 1.68e-05
VT+G4 -1567.362 3158.723 - 7.14e-06 3160.875 - 7.93e-06 3195.474 - 1.2e-05
Q.pfam+I+G4 -1565.117 3156.233 - 2.48e-05 3158.761 - 2.28e-05 3196.047 - 9.04e-06
JTTDCMut+I -1567.879 3159.758 - 4.26e-06 3161.910 - 4.73e-06 3196.509 - 7.17e-06
VT+I -1568.081 3160.163 - 3.48e-06 3162.314 - 3.86e-06 3196.914 - 5.86e-06
JTT+I -1568.353 3160.707 - 2.65e-06 3162.859 - 2.94e-06 3197.458 - 4.46e-06
JTTDCMut+I+G4 -1566.061 3158.122 - 9.65e-06 3160.650 - 8.87e-06 3197.936 - 3.52e-06
Q.pfam+I -1568.603 3161.206 - 2.06e-06 3163.358 - 2.29e-06 3197.957 - 3.48e-06
LG+R2 -1566.272 3158.544 - 7.81e-06 3161.072 - 7.18e-06 3198.358 - 2.85e-06
JTTDCMut+R2 -1566.344 3158.688 - 7.27e-06 3161.216 - 6.69e-06 3198.502 - 2.65e-06
JTT+I+G4 -1566.596 3159.192 - 5.65e-06 3161.719 - 5.2e-06 3199.005 - 2.06e-06
LG+I+G4 -1566.772 3159.544 - 4.74e-06 3162.072 - 4.36e-06 3199.358 - 1.73e-06
JTT+R2 -1566.893 3159.787 - 4.2e-06 3162.315 - 3.86e-06 3199.601 - 1.53e-06
VT+R2 -1566.950 3159.900 - 3.97e-06 3162.428 - 3.65e-06 3199.714 - 1.44e-06
Q.pfam+I+R2 -1564.544 3157.089 - 1.62e-05 3160.026 - 1.21e-05 3199.965 - 1.27e-06
VT+I+G4 -1567.208 3160.416 - 3.06e-06 3162.944 - 2.82e-06 3200.229 - 1.12e-06
LG+I -1570.140 3164.281 - 4.44e-07 3166.432 - 4.93e-07 3201.032 - 7.48e-07
DCMut+G4 -1570.880 3165.761 - 2.12e-07 3167.912 - 2.35e-07 3202.512 - 3.57e-07
Dayhoff+G4 -1570.881 3165.762 - 2.12e-07 3167.914 - 2.35e-07 3202.514 - 3.56e-07
JTTDCMut+I+R2 -1565.956 3159.911 - 3.94e-06 3162.849 - 2.96e-06 3202.788 - 3.11e-07
LG+I+R2 -1566.303 3160.605 - 2.79e-06 3163.542 - 2.09e-06 3203.482 - 2.2e-07
JTT+I+R2 -1566.496 3160.992 - 2.3e-06 3163.929 - 1.72e-06 3203.868 - 1.81e-07
VT+I+R2 -1566.946 3161.891 - 1.47e-06 3164.828 - 1.1e-06 3204.767 - 1.15e-07
DCMut+R2 -1570.698 3167.397 - 9.34e-08 3169.925 - 8.59e-08 3207.211 - 3.4e-08
Dayhoff+R2 -1570.702 3167.403 - 9.31e-08 3169.931 - 8.56e-08 3207.217 - 3.39e-08
DCMut+I+G4 -1570.768 3167.537 - 8.71e-08 3170.065 - 8.01e-08 3207.351 - 3.17e-08
Dayhoff+I+G4 -1570.770 3167.540 - 8.7e-08 3170.068 - 8e-08 3207.353 - 3.17e-08
LG -1575.931 3173.862 - 3.69e-09 3175.670 - 4.86e-09 3207.551 - 2.87e-08
LG+R3 -1566.442 3162.884 - 8.92e-07 3166.265 - 5.36e-07 3208.823 - 1.52e-08
DCMut+I -1574.744 3173.488 - 4.44e-09 3175.640 - 4.93e-09 3210.239 - 7.49e-09
Dayhoff+I -1574.789 3173.578 - 4.25e-09 3175.730 - 4.72e-09 3210.329 - 7.16e-09
DCMut+I+R2 -1570.474 3168.948 - 4.3e-08 3171.886 - 3.22e-08 3211.825 - 3.39e-09
Dayhoff+I+R2 -1570.475 3168.950 - 4.3e-08 3171.887 - 3.22e-08 3211.826 - 3.39e-09
PMB+G4 -1576.467 3176.935 - 7.93e-10 3179.086 - 8.8e-10 3213.686 - 1.34e-09
LG+I+R3 -1566.552 3165.103 - 2.94e-07 3168.962 - 1.39e-07 3214.105 - 1.08e-09
PMB+I -1577.684 3179.368 - 2.35e-10 3181.520 - 2.61e-10 3216.120 - 3.96e-10
PMB+R2 -1576.050 3178.100 - 4.43e-10 3180.628 - 4.07e-10 3217.914 - 1.61e-10
Blosum62+G4 -1578.643 3181.287 - 9e-11 3183.439 - 9.99e-11 3218.038 - 1.52e-10
PMB+I+G4 -1576.527 3179.054 - 2.75e-10 3181.581 - 2.53e-10 3218.867 - 1e-10
Blosum62+I -1580.029 3184.058 - 2.25e-11 3186.210 - 2.5e-11 3220.809 - 3.79e-11
Blosum62+R2 -1578.166 3182.331 - 5.34e-11 3184.859 - 4.91e-11 3222.145 - 1.95e-11
PMB+I+R2 -1576.160 3180.320 - 1.46e-10 3183.257 - 1.09e-10 3223.196 - 1.15e-11
Blosum62+I+G4 -1578.692 3183.384 - 3.15e-11 3185.912 - 2.9e-11 3223.198 - 1.15e-11
Blosum62+I+R2 -1578.280 3184.559 - 1.75e-11 3187.497 - 1.31e-11 3227.436 - 1.38e-12
WAG+F+G4 -1553.748 3169.495 - 3.27e-08 3185.241 - 4.06e-11 3264.436 - 1.28e-20
WAG+F+I -1554.925 3171.851 - 1.01e-08 3187.597 - 1.25e-11 3266.791 - 3.93e-21
WAG+F+R2 -1553.291 3170.582 - 1.9e-08 3187.478 - 1.33e-11 3268.585 - 1.6e-21
WAG+F+I+G4 -1553.741 3171.483 - 1.21e-08 3188.379 - 8.45e-12 3269.486 - 1.02e-21
LG+F+G4 -1557.273 3176.547 - 9.63e-10 3192.293 - 1.19e-12 3271.487 - 3.75e-22
WAG+F+I+R2 -1553.368 3172.736 - 6.47e-09 3190.832 - 2.48e-12 3273.801 - 1.18e-22
Q.pfam+F+G4 -1558.967 3179.935 - 1.77e-10 3195.681 - 2.19e-13 3274.875 - 6.9e-23
LG+F+R2 -1557.103 3178.205 - 4.2e-10 3195.101 - 2.93e-13 3276.208 - 3.54e-23
LG+F+I+G4 -1557.433 3178.865 - 3.02e-10 3195.761 - 2.11e-13 3276.868 - 2.55e-23
LG+F+I -1560.234 3182.469 - 4.98e-11 3198.215 - 6.18e-14 3277.409 - 1.94e-23
DCMut+F+G4 -1560.641 3183.282 - 3.32e-11 3199.028 - 4.11e-14 3278.223 - 1.29e-23
Dayhoff+F+G4 -1560.668 3183.336 - 3.23e-11 3199.082 - 4.01e-14 3278.276 - 1.26e-23
Q.pfam+F+R2 -1558.711 3181.423 - 8.41e-11 3198.319 - 5.87e-14 3279.426 - 7.09e-24
JTTDCMut+F+G4 -1561.252 3184.504 - 1.8e-11 3200.250 - 2.23e-14 3279.445 - 7.02e-24
VT+F+G4 -1561.435 3184.869 - 1.5e-11 3200.615 - 1.86e-14 3279.810 - 5.85e-24
JTT+F+G4 -1561.570 3185.141 - 1.31e-11 3200.887 - 1.62e-14 3280.081 - 5.11e-24
Q.pfam+F+I+G4 -1559.298 3182.596 - 4.68e-11 3199.492 - 3.26e-14 3280.599 - 3.94e-24
VT+F+I -1561.921 3185.841 - 9.23e-12 3201.587 - 1.14e-14 3280.782 - 3.6e-24
LG+F+I+R2 -1557.083 3180.167 - 1.58e-10 3198.264 - 6.03e-14 3281.233 - 2.87e-24
Q.pfam+F+I -1562.180 3186.361 - 7.12e-12 3202.107 - 8.83e-15 3281.301 - 2.78e-24
JTTDCMut+F+I -1562.339 3186.679 - 6.07e-12 3202.425 - 7.53e-15 3281.619 - 2.37e-24
JTT+F+I -1562.570 3187.141 - 4.82e-12 3202.887 - 5.98e-15 3282.081 - 1.88e-24
DCMut+F+R2 -1560.362 3184.724 - 1.61e-11 3201.620 - 1.13e-14 3282.727 - 1.36e-24
Dayhoff+F+R2 -1560.386 3184.771 - 1.58e-11 3201.667 - 1.1e-14 3282.774 - 1.33e-24
DCMut+F+I+G4 -1560.654 3185.308 - 1.21e-11 3202.204 - 8.41e-15 3283.311 - 1.02e-24
Dayhoff+F+I+G4 -1560.677 3185.355 - 1.18e-11 3202.251 - 8.21e-15 3283.358 - 9.93e-25
JTTDCMut+F+I+G4 -1560.864 3185.727 - 9.77e-12 3202.623 - 6.82e-15 3283.730 - 8.24e-25
VT+F+R2 -1561.067 3186.134 - 7.97e-12 3203.030 - 5.56e-15 3284.137 - 6.72e-25
JTTDCMut+F+R2 -1561.132 3186.264 - 7.47e-12 3203.160 - 5.21e-15 3284.267 - 6.3e-25
JTT+F+I+G4 -1561.162 3186.324 - 7.25e-12 3203.220 - 5.06e-15 3284.327 - 6.11e-25
VT+F+I+G4 -1561.277 3186.554 - 6.46e-12 3203.450 - 4.51e-15 3284.557 - 5.45e-25
Q.pfam+F+I+R2 -1558.838 3183.676 - 2.72e-11 3201.773 - 1.04e-14 3284.742 - 4.97e-25
JTT+F+R2 -1561.452 3186.905 - 5.42e-12 3203.801 - 3.78e-15 3284.908 - 4.57e-25
DCMut+F+I -1564.311 3190.622 - 8.46e-13 3206.368 - 1.05e-15 3285.562 - 3.3e-25
Dayhoff+F+I -1564.369 3190.739 - 7.98e-13 3206.485 - 9.89e-16 3285.679 - 3.11e-25
DCMut+F+I+R2 -1560.361 3186.721 - 5.95e-12 3204.818 - 2.28e-15 3287.787 - 1.08e-25
Dayhoff+F+I+R2 -1560.384 3186.768 - 5.81e-12 3204.865 - 2.22e-15 3287.834 - 1.06e-25
JTTDCMut+F+I+R2 -1560.796 3187.593 - 3.85e-12 3205.689 - 1.47e-15 3288.658 - 7.01e-26
VT+F+I+R2 -1561.054 3188.109 - 2.97e-12 3206.206 - 1.14e-15 3289.174 - 5.42e-26
JTT+F+I+R2 -1561.102 3188.204 - 2.83e-12 3206.301 - 1.08e-15 3289.270 - 5.16e-26
Blosum62+F+G4 -1569.223 3200.447 - 6.22e-15 3216.193 - 7.71e-18 3295.387 - 2.42e-27
PMB+F+G4 -1570.183 3202.367 - 2.38e-15 3218.113 - 2.95e-18 3297.307 - 9.28e-28
Blosum62+F+I -1570.243 3202.486 - 2.24e-15 3218.232 - 2.78e-18 3297.426 - 8.75e-28
PMB+F+I -1571.137 3204.274 - 9.18e-16 3220.020 - 1.14e-18 3299.214 - 3.58e-28
Blosum62+F+R2 -1568.765 3201.529 - 3.62e-15 3218.425 - 2.53e-18 3299.532 - 3.05e-28
Blosum62+F+I+G4 -1569.227 3202.454 - 2.28e-15 3219.350 - 1.59e-18 3300.457 - 1.92e-28
PMB+F+R2 -1569.803 3203.606 - 1.28e-15 3220.502 - 8.94e-19 3301.609 - 1.08e-28
PMB+F+I+G4 -1570.207 3204.413 - 8.56e-16 3221.309 - 5.97e-19 3302.416 - 7.22e-29
Blosum62+F+I+R2 -1568.859 3203.717 - 1.21e-15 3221.814 - 4.64e-19 3304.783 - 2.21e-29
PMB+F+I+R2 -1569.900 3205.800 - 4.28e-16 3223.897 - 1.64e-19 3306.865 - 7.8e-30
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+G4
State frequencies: (model)
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 2.5747
Category Relative_rate Proportion
1 0.3534 0.2500
2 0.7049 0.2500
3 1.0794 0.2500
4 1.8623 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: -1556.4179 (s.e. 52.9386)
Unconstrained log-likelihood (without tree): -794.3448
Number of free parameters (#branches + #model parameters): 12
Akaike information criterion (AIC) score: 3136.8358
Corrected Akaike information criterion (AICc) score: 3138.9875
Bayesian information criterion (BIC) score: 3173.5869
Total tree length (sum of branch lengths): 3.1219
Sum of internal branch lengths: 0.4838 (15.4968% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'PYVX_18179' is drawn at root
+---------------------------------------PYVX_18179
|
| +-------------------------------------PHALS_06480
| +--|
| | +--PHYKE_8390
| +--|
| | +--PHYRA_81105
| +----|
| | +--PHYSO_353401
+--------|
| +--------HYAP_07096
|
+--------------------PYU1_G001738
Tree in newick format:
(PYVX_18179:0.9150576917,((((PHALS_06480:0.8688068739,PHYKE_8390:0.0639669619):0.0894000711,PHYRA_81105:0.0475645034):0.0511657606,PHYSO_353401:0.0428087006):0.1235969409,HYAP_07096:0.2198359657):0.2196321656,PYU1_G001738:0.4800691378);
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+G4{2.57473}" --length 158
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 19 06:09:24 2024
Total CPU time used: 9.97002 seconds (0h:0m:9s)
Total wall-clock time used: 3.42221 seconds (0h:0m:3s)