(HYAP_01511:0.8157917903,(PYAR_14487:0.0894844012,PHYKE_6984:0.0044003502):0.0115371813,((PHYRA_72415:0.0261102553,PHYCA_532912:0.0297567993):0.0100343869,PHYSO_480010:0.0133068969):0.0000021259);
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: 334015
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: 6 sequences with 652 amino-acid sites
Number of constant sites: 497 (= 76.227% of all sites)
Number of invariant (constant or ambiguous constant) sites: 497 (= 76.227% of all sites)
Number of parsimony informative sites: 15
Number of distinct site patterns: 254
ModelFinder
-----------
Best-fit model according to BIC: Q.pfam+I
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
Q.pfam+I -2843.897 5707.794 + 0.359 5708.137 + 0.371 5752.595 + 0.503
LG+I -2844.535 5709.070 + 0.19 5709.413 + 0.196 5753.870 + 0.266
Q.pfam+G4 -2845.295 5710.591 + 0.0886 5710.934 + 0.0917 5755.391 + 0.124
LG+G4 -2845.910 5711.821 - 0.0479 5712.164 - 0.0496 5756.621 + 0.0671
Q.pfam+I+G4 -2844.061 5710.123 + 0.112 5710.535 + 0.112 5759.403 - 0.0167
LG+I+G4 -2844.634 5711.269 + 0.0631 5711.681 + 0.0631 5760.549 - 0.00942
Q.pfam+R2 -2844.830 5711.661 + 0.0519 5712.073 + 0.0519 5760.941 - 0.00774
LG+R2 -2845.347 5712.693 - 0.031 5713.106 - 0.031 5761.974 - 0.00462
LG -2852.910 5723.819 - 0.000119 5724.100 - 0.000127 5764.140 - 0.00156
LG+I+R2 -2844.840 5713.680 - 0.0189 5714.169 - 0.0182 5767.441 - 0.0003
WAG+I -2851.959 5723.918 - 0.000113 5724.261 - 0.000117 5768.718 - 0.000158
WAG+G4 -2852.902 5725.803 - 4.41e-05 5726.146 - 4.56e-05 5770.604 - 6.17e-05
VT+I -2853.549 5727.099 - 2.3e-05 5727.442 - 2.39e-05 5771.899 - 3.23e-05
VT+G4 -2854.499 5728.998 - 8.92e-06 5729.341 - 9.23e-06 5773.799 - 1.25e-05
LG+R3 -2845.481 5716.962 - 0.00366 5717.533 - 0.00338 5775.203 - 6.19e-06
WAG+I+G4 -2852.138 5726.276 - 3.48e-05 5726.689 - 3.48e-05 5775.557 - 5.19e-06
WAG+R2 -2852.591 5727.181 - 2.21e-05 5727.594 - 2.21e-05 5776.462 - 3.3e-06
JTT+I -2856.608 5733.215 - 1.08e-06 5733.559 - 1.12e-06 5778.016 - 1.52e-06
JTTDCMut+I -2857.042 5734.083 - 7.01e-07 5734.427 - 7.26e-07 5778.884 - 9.83e-07
VT+I+G4 -2853.940 5729.879 - 5.74e-06 5730.292 - 5.74e-06 5779.160 - 8.56e-07
VT+R2 -2854.234 5730.469 - 4.27e-06 5730.881 - 4.27e-06 5779.749 - 6.38e-07
JTT+G4 -2857.606 5735.211 - 3.99e-07 5735.554 - 4.13e-07 5780.012 - 5.59e-07
LG+I+R3 -2844.785 5717.570 - 0.0027 5718.229 - 0.00239 5780.290 - 4.87e-07
JTTDCMut+G4 -2858.022 5736.045 - 2.63e-07 5736.388 - 2.72e-07 5780.845 - 3.69e-07
JTT+I+G4 -2856.753 5735.507 - 3.44e-07 5735.919 - 3.44e-07 5784.787 - 5.14e-08
JTTDCMut+I+G4 -2857.187 5736.373 - 2.23e-07 5736.786 - 2.23e-07 5785.654 - 3.33e-08
JTT+R2 -2857.271 5736.542 - 2.05e-07 5736.954 - 2.05e-07 5785.822 - 3.06e-08
JTTDCMut+R2 -2857.688 5737.376 - 1.35e-07 5737.788 - 1.35e-07 5786.656 - 2.02e-08
Blosum62+I -2865.430 5750.861 - 1.6e-10 5751.204 - 1.65e-10 5795.661 - 2.24e-10
Blosum62+G4 -2866.530 5753.061 - 5.31e-11 5753.404 - 5.5e-11 5797.861 - 7.44e-11
Blosum62+I+G4 -2865.747 5753.494 - 4.28e-11 5753.906 - 4.27e-11 5802.774 - 6.38e-12
Blosum62+R2 -2866.237 5754.473 - 2.62e-11 5754.886 - 2.62e-11 5803.754 - 3.91e-12
PMB+I -2874.137 5768.275 - 2.64e-14 5768.618 - 2.73e-14 5813.075 - 3.7e-14
PMB+G4 -2875.036 5770.073 - 1.07e-14 5770.416 - 1.11e-14 5814.873 - 1.5e-14
PMB+I+G4 -2874.385 5770.771 - 7.58e-15 5771.183 - 7.57e-15 5820.051 - 1.13e-15
PMB+R2 -2874.796 5771.593 - 5.02e-15 5772.005 - 5.02e-15 5820.873 - 7.49e-16
Dayhoff+I -2878.857 5777.713 - 2.35e-16 5778.056 - 2.44e-16 5822.513 - 3.3e-16
DCMut+I -2878.936 5777.872 - 2.17e-16 5778.216 - 2.25e-16 5822.673 - 3.05e-16
Dayhoff+G4 -2878.953 5777.906 - 2.14e-16 5778.249 - 2.21e-16 5822.707 - 3e-16
DCMut+G4 -2879.041 5778.081 - 1.96e-16 5778.425 - 2.03e-16 5822.882 - 2.74e-16
Dayhoff+I+G4 -2878.802 5779.605 - 9.14e-17 5780.017 - 9.14e-17 5828.885 - 1.36e-17
Dayhoff+R2 -2878.878 5779.756 - 8.48e-17 5780.168 - 8.48e-17 5829.036 - 1.26e-17
DCMut+I+G4 -2878.887 5779.774 - 8.4e-17 5780.187 - 8.4e-17 5829.055 - 1.25e-17
DCMut+R2 -2878.935 5779.871 - 8.01e-17 5780.283 - 8e-17 5829.151 - 1.19e-17
LG+F+I -2828.081 5714.163 - 0.0148 5716.960 - 0.0045 5844.084 - 6.83e-21
LG+F+G4 -2829.175 5716.350 - 0.00497 5719.147 - 0.00151 5846.271 - 2.29e-21
Q.pfam+F+I -2829.871 5717.741 - 0.00248 5720.539 - 0.000753 5847.662 - 1.14e-21
Q.pfam+F+G4 -2831.147 5720.294 - 0.000692 5723.091 - 0.00021 5850.215 - 3.19e-22
LG+F+I+G4 -2828.213 5716.425 - 0.00479 5719.420 - 0.00132 5850.827 - 2.35e-22
LG+F+R2 -2828.708 5717.416 - 0.00292 5720.411 - 0.000802 5851.817 - 1.43e-22
Q.pfam+F+I+G4 -2830.048 5720.095 - 0.000765 5723.090 - 0.00021 5854.497 - 3.74e-23
Q.pfam+F+R2 -2830.723 5721.447 - 0.000389 5724.442 - 0.000107 5855.848 - 1.91e-23
VT+F+I -2841.247 5740.494 - 2.84e-08 5743.291 - 8.63e-09 5870.415 - 1.31e-26
VT+F+G4 -2842.124 5742.248 - 1.18e-08 5745.045 - 3.59e-09 5872.169 - 5.44e-27
WAG+F+I -2842.603 5743.205 - 7.33e-09 5746.003 - 2.22e-09 5873.127 - 3.37e-27
WAG+F+G4 -2843.627 5745.255 - 2.63e-09 5748.052 - 7.98e-10 5875.176 - 1.21e-27
Blosum62+F+I -2843.656 5745.312 - 2.56e-09 5748.110 - 7.76e-10 5875.234 - 1.18e-27
Blosum62+F+G4 -2844.648 5747.297 - 9.48e-10 5750.094 - 2.88e-10 5877.218 - 4.36e-28
VT+F+I+G4 -2841.634 5743.269 - 7.1e-09 5746.264 - 1.95e-09 5877.670 - 3.48e-28
VT+F+R2 -2841.881 5743.762 - 5.55e-09 5746.757 - 1.52e-09 5878.164 - 2.72e-28
WAG+F+I+G4 -2842.759 5745.519 - 2.31e-09 5748.514 - 6.34e-10 5879.920 - 1.13e-28
WAG+F+R2 -2843.277 5746.554 - 1.37e-09 5749.549 - 3.78e-10 5880.956 - 6.73e-29
JTT+F+I -2846.988 5751.977 - 9.13e-11 5754.774 - 2.77e-11 5881.898 - 4.2e-29
Blosum62+F+I+G4 -2843.965 5747.929 - 6.91e-10 5750.924 - 1.9e-10 5882.330 - 3.38e-29
JTTDCMut+F+I -2847.507 5753.015 - 5.43e-11 5755.812 - 1.65e-11 5882.936 - 2.5e-29
Blosum62+F+R2 -2844.385 5748.769 - 4.54e-10 5751.764 - 1.25e-10 5883.171 - 2.22e-29
JTT+F+G4 -2847.963 5753.927 - 3.44e-11 5756.724 - 1.04e-11 5883.848 - 1.58e-29
JTTDCMut+F+G4 -2848.472 5754.944 - 2.07e-11 5757.742 - 6.28e-12 5884.866 - 9.53e-30
PMB+F+I -2849.517 5757.035 - 7.28e-12 5759.832 - 2.21e-12 5886.956 - 3.35e-30
JTT+F+I+G4 -2847.134 5754.267 - 2.9e-11 5757.262 - 7.98e-12 5888.669 - 1.42e-30
PMB+F+G4 -2850.385 5758.770 - 3.06e-12 5761.567 - 9.28e-13 5888.691 - 1.41e-30
JTTDCMut+F+I+G4 -2847.620 5755.240 - 1.79e-11 5758.236 - 4.91e-12 5889.642 - 8.75e-31
JTT+F+R2 -2847.630 5755.261 - 1.77e-11 5758.256 - 4.86e-12 5889.662 - 8.66e-31
JTTDCMut+F+R2 -2848.139 5756.277 - 1.06e-11 5759.273 - 2.92e-12 5890.679 - 5.21e-31
PMB+F+I+G4 -2849.714 5759.428 - 2.2e-12 5762.423 - 6.05e-13 5893.829 - 1.08e-31
PMB+F+R2 -2850.158 5760.316 - 1.41e-12 5763.311 - 3.88e-13 5894.717 - 6.91e-32
Dayhoff+F+I -2858.453 5774.907 - 9.58e-16 5777.704 - 2.91e-16 5904.828 - 4.41e-34
DCMut+F+I -2858.498 5774.996 - 9.16e-16 5777.794 - 2.78e-16 5904.918 - 4.21e-34
Dayhoff+F+G4 -2858.605 5775.210 - 8.23e-16 5778.008 - 2.5e-16 5905.132 - 3.79e-34
DCMut+F+G4 -2858.655 5775.310 - 7.83e-16 5778.107 - 2.38e-16 5905.231 - 3.6e-34
Dayhoff+F+I+G4 -2858.353 5776.705 - 3.9e-16 5779.700 - 1.07e-16 5911.106 - 1.91e-35
DCMut+F+I+G4 -2858.402 5776.804 - 3.71e-16 5779.799 - 1.02e-16 5911.205 - 1.82e-35
Dayhoff+F+R2 -2858.796 5777.592 - 2.5e-16 5780.588 - 6.87e-17 5911.994 - 1.22e-35
DCMut+F+R2 -2858.845 5777.691 - 2.38e-16 5780.686 - 6.54e-17 5912.092 - 1.17e-35
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: Q.pfam+I
State frequencies: (model)
Model of rate heterogeneity: Invar
Proportion of invariable sites: 0.3391
Category Relative_rate Proportion
0 0 0.3391
1 1.5131 0.6609
MAXIMUM LIKELIHOOD TREE
-----------------------
Log-likelihood of the tree: -2843.8971 (s.e. 65.9337)
Unconstrained log-likelihood (without tree): -3309.1918
Number of free parameters (#branches + #model parameters): 10
Akaike information criterion (AIC) score: 5707.7941
Corrected Akaike information criterion (AICc) score: 5708.1373
Bayesian information criterion (BIC) score: 5752.5946
Total tree length (sum of branch lengths): 1.0004
Sum of internal branch lengths: 0.0216 (2.1565% of tree length)
WARNING: 1 near-zero internal branches (<0.0015) should be treated with caution
Such branches are denoted by '**' in the figure below
NOTE: Tree is UNROOTED although outgroup taxon 'HYAP_01511' is drawn at root
+-----------------------------------------------------------HYAP_01511
|
| +-----PYAR_14487
+--|
| +--PHYKE_6984
|
| +--PHYRA_72415
| +--|
| | +--PHYCA_532912
+**|
+--PHYSO_480010
Tree in newick format:
(HYAP_01511:0.8157917903,(PYAR_14487:0.0894844012,PHYKE_6984:0.0044003502):0.0115371813,((PHYRA_72415:0.0261102553,PHYCA_532912:0.0297567993):0.0100343869,PHYSO_480010:0.0133068969):0.0000021259);
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 "Q.pfam+I{0.339086}" --length 652
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 15:26:06 2024
Total CPU time used: 3.08531 seconds (0h:0m:3s)
Total wall-clock time used: 1.08634 seconds (0h:0m:1s)