(PYVX_15863:1.3665825334,(((((HYAP_01513:0.9436198203,PHALS_10835:0.3489977653):0.0857584545,PHYCA_504706:0.1390152218):0.0391494707,PITG_00011:0.0285433735):0.0232556155,PPTG_16672:0.0964824381):0.0844725067,PHYSO_478253:0.1280065106):0.0153746344,PHYKE_5720:0.3893190554);
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: 702476
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 240 amino-acid sites
Number of constant sites: 47 (= 19.5833% of all sites)
Number of invariant (constant or ambiguous constant) sites: 47 (= 19.5833% of all sites)
Number of parsimony informative sites: 52
Number of distinct site patterns: 213
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 -2584.996 5197.991 - 1.05e-14 5199.858 - 1.05e-12 5246.720 + 0.577
Q.pfam+F+G4 -2534.263 5134.526 + 0.636 5145.419 + 0.696 5249.387 + 0.152
JTTDCMut+G4 -2586.510 5201.020 - 2.31e-15 5202.887 - 2.31e-13 5249.749 + 0.127
VT+G4 -2587.559 5203.119 - 8.11e-16 5204.985 - 8.09e-14 5251.848 - 0.0444
JTT+I+G4 -2585.003 5200.006 - 3.84e-15 5202.149 - 3.34e-13 5252.215 - 0.0369
JTT+R2 -2585.905 5201.809 - 1.56e-15 5203.952 - 1.36e-13 5254.019 - 0.015
VT+F+G4 -2537.049 5140.099 - 0.0392 5150.992 - 0.0429 5254.960 - 0.00937
JTTDCMut+I+G4 -2586.517 5203.033 - 8.46e-16 5205.176 - 7.35e-14 5255.243 - 0.00813
Q.pfam+F+I+G4 -2534.605 5137.210 + 0.166 5148.820 + 0.127 5255.552 - 0.00697
JTT+F+G4 -2537.390 5140.780 - 0.0279 5151.673 - 0.0305 5255.641 - 0.00666
Q.pfam+F+R2 -2535.319 5138.639 + 0.0814 5150.249 + 0.0622 5256.981 - 0.00341
JTTDCMut+R2 -2587.402 5204.803 - 3.49e-16 5206.946 - 3.03e-14 5257.013 - 0.00336
VT+I+G4 -2587.446 5204.893 - 3.34e-16 5207.036 - 2.9e-14 5257.102 - 0.00321
VT+R2 -2587.618 5205.235 - 2.81e-16 5207.378 - 2.44e-14 5257.445 - 0.0027
JTTDCMut+F+G4 -2538.308 5142.617 - 0.0111 5153.510 - 0.0122 5257.478 - 0.00266
VT+F+I+G4 -2537.263 5142.527 - 0.0116 5154.136 - 0.0089 5260.868 - 0.000488
VT+F+R2 -2537.463 5142.925 - 0.00954 5154.535 - 0.00729 5261.267 - 0.0004
JTT+F+I+G4 -2537.563 5143.126 - 0.00863 5154.736 - 0.00659 5261.468 - 0.000362
WAG+F+G4 -2540.613 5147.226 - 0.00111 5158.119 - 0.00122 5262.087 - 0.000265
JTTDCMut+F+I+G4 -2538.509 5145.019 - 0.00335 5156.628 - 0.00256 5263.360 - 0.00014
LG+F+G4 -2541.610 5149.220 - 0.00041 5160.113 - 0.000448 5264.081 - 9.79e-05
JTT+F+R2 -2538.967 5145.933 - 0.00212 5157.543 - 0.00162 5264.275 - 8.89e-05
WAG+G4 -2593.955 5215.910 - 1.35e-18 5217.777 - 1.35e-16 5264.639 - 7.41e-05
JTTDCMut+F+R2 -2539.906 5147.811 - 0.000829 5159.421 - 0.000634 5266.153 - 3.48e-05
WAG+F+I+G4 -2541.117 5150.233 - 0.000247 5161.843 - 0.000189 5268.575 - 1.04e-05
Q.pfam+G4 -2596.202 5220.403 - 1.43e-19 5222.270 - 1.43e-17 5269.132 - 7.84e-06
WAG+F+R2 -2541.522 5151.043 - 0.000165 5162.653 - 0.000126 5269.385 - 6.9e-06
WAG+I+G4 -2594.089 5218.178 - 4.35e-19 5220.321 - 3.78e-17 5270.388 - 4.18e-06
LG+F+I+G4 -2542.029 5152.058 - 9.92e-05 5163.668 - 7.58e-05 5270.400 - 4.16e-06
WAG+R2 -2594.612 5219.225 - 2.58e-19 5221.368 - 2.24e-17 5271.435 - 2.48e-06
LG+F+R2 -2543.413 5154.826 - 2.49e-05 5166.436 - 1.9e-05 5273.168 - 1.04e-06
Q.pfam+I+G4 -2596.240 5222.481 - 5.06e-20 5224.624 - 4.4e-18 5274.690 - 4.87e-07
Q.pfam+R2 -2596.862 5223.724 - 2.72e-20 5225.867 - 2.36e-18 5275.933 - 2.61e-07
DCMut+F+G4 -2550.993 5167.986 - 3.45e-08 5178.879 - 3.77e-08 5282.847 - 8.24e-09
Dayhoff+F+G4 -2551.263 5168.526 - 2.63e-08 5179.419 - 2.88e-08 5283.387 - 6.29e-09
LG+G4 -2605.240 5238.480 - 1.7e-23 5240.347 - 1.69e-21 5287.209 - 9.31e-10
PMB+F+G4 -2553.445 5172.890 - 2.97e-09 5183.784 - 3.25e-09 5287.752 - 7.09e-10
DCMut+F+I+G4 -2551.399 5170.798 - 8.45e-09 5182.408 - 6.46e-09 5289.140 - 3.54e-10
Dayhoff+F+I+G4 -2551.671 5171.342 - 6.44e-09 5182.951 - 4.92e-09 5289.683 - 2.7e-10
DCMut+G4 -2607.244 5242.488 - 2.29e-24 5244.354 - 2.28e-22 5291.216 - 1.25e-10
Dayhoff+G4 -2607.464 5242.929 - 1.84e-24 5244.795 - 1.83e-22 5291.658 - 1.01e-10
DCMut+F+R2 -2553.216 5174.431 - 1.37e-09 5186.041 - 1.05e-09 5292.773 - 5.76e-11
LG+I+G4 -2605.381 5240.763 - 5.43e-24 5242.905 - 4.72e-22 5292.972 - 5.22e-11
Dayhoff+F+R2 -2553.524 5175.047 - 1.01e-09 5186.657 - 7.72e-10 5293.389 - 4.23e-11
PMB+F+I+G4 -2553.843 5175.686 - 7.34e-10 5187.296 - 5.61e-10 5294.028 - 3.08e-11
PMB+F+R2 -2553.926 5175.851 - 6.76e-10 5187.461 - 5.17e-10 5294.193 - 2.83e-11
LG+R2 -2606.613 5243.226 - 1.58e-24 5245.369 - 1.38e-22 5295.436 - 1.52e-11
Blosum62+F+G4 -2557.890 5181.779 - 3.49e-11 5192.672 - 3.81e-11 5296.640 - 8.33e-12
DCMut+I+G4 -2607.434 5244.868 - 6.97e-25 5247.011 - 6.05e-23 5297.078 - 6.69e-12
Dayhoff+I+G4 -2607.658 5245.317 - 5.57e-25 5247.459 - 4.84e-23 5297.526 - 5.35e-12
LG+I+R2 -2605.749 5243.497 - 1.38e-24 5245.937 - 1.04e-22 5299.187 - 2.33e-12
DCMut+R2 -2608.692 5247.385 - 1.98e-25 5249.528 - 1.72e-23 5299.594 - 1.9e-12
Dayhoff+R2 -2608.950 5247.900 - 1.53e-25 5250.043 - 1.33e-23 5300.110 - 1.47e-12
Blosum62+F+I+G4 -2558.258 5184.516 - 8.88e-12 5196.125 - 6.79e-12 5302.857 - 3.72e-13
Blosum62+F+R2 -2558.398 5184.795 - 7.72e-12 5196.405 - 5.9e-12 5303.137 - 3.24e-13
LG+R3 -2605.372 5244.745 - 7.41e-25 5247.501 - 4.74e-23 5303.916 - 2.19e-13
LG+I+R3 -2605.012 5246.024 - 3.91e-25 5249.119 - 2.11e-23 5308.675 - 2.03e-14
LG+I -2616.869 5261.738 - 1.51e-28 5263.605 - 1.51e-26 5310.467 - 8.29e-15
PMB+G4 -2619.921 5267.842 - 7.15e-30 5269.709 - 7.13e-28 5316.571 - 3.92e-16
PMB+I+G4 -2619.866 5269.731 - 2.78e-30 5271.874 - 2.42e-28 5321.941 - 2.67e-17
PMB+R2 -2619.868 5269.737 - 2.77e-30 5271.880 - 2.41e-28 5321.946 - 2.66e-17
LG -2633.730 5293.459 - 1.96e-35 5295.070 - 2.22e-33 5338.707 - 6.11e-21
Blosum62+G4 -2635.998 5299.996 - 7.45e-37 5301.863 - 7.43e-35 5348.725 - 4.08e-23
Blosum62+I+G4 -2635.824 5301.647 - 3.26e-37 5303.790 - 2.83e-35 5353.857 - 3.14e-24
Blosum62+R2 -2636.118 5302.236 - 2.43e-37 5304.378 - 2.11e-35 5354.445 - 2.34e-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: JTT+G4
State frequencies: (model)
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 1.3507
Category Relative_rate Proportion
1 0.2013 0.2500
2 0.5617 0.2500
3 1.0403 0.2500
4 2.1967 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: -2584.7941 (s.e. 74.3257)
Unconstrained log-likelihood (without tree): -1262.7613
Number of free parameters (#branches + #model parameters): 14
Akaike information criterion (AIC) score: 5197.5881
Corrected Akaike information criterion (AICc) score: 5199.4548
Bayesian information criterion (BIC) score: 5246.3171
Total tree length (sum of branch lengths): 3.6886
Sum of internal branch lengths: 0.2480 (6.7237% of tree length)
NOTE: Tree is UNROOTED although outgroup taxon 'PYVX_15863' is drawn at root
+-----------------------------------------------------------PYVX_15863
|
| +----------------------------------------HYAP_01513
| +--|
| | +--------------PHALS_10835
| +--|
| | +-----PHYCA_504706
| +--|
| | +--PITG_00011
| +--|
| | +---PPTG_16672
+--|
| +----PHYSO_478253
|
+----------------PHYKE_5720
Tree in newick format:
(PYVX_15863:1.3665825334,(((((HYAP_01513:0.9436198203,PHALS_10835:0.3489977653):0.0857584545,PHYCA_504706:0.1390152218):0.0391494707,PITG_00011:0.0285433735):0.0232556155,PPTG_16672:0.0964824381):0.0844725067,PHYSO_478253:0.1280065106):0.0153746344,PHYKE_5720:0.3893190554);
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{1.35067}" --length 240
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: Thu Apr 25 03:49:38 2024
Total CPU time used: 12.2764 seconds (0h:0m:12s)
Total wall-clock time used: 4.18934 seconds (0h:0m:4s)