Newick Format
(CCA17542:0.0761441386,CCI44820:0.2135054929,((PYAP_17747:0.2594317776,((PYU1_G001736:0.1498063812,((SPRG_06335:0.0212011740,SDRG_01782:0.0477137238):0.1527800510,(H257_06293:0.0850061078,H310_09224:0.1422366964):0.4316060840):0.6298215409):0.0652865570,(PYIR_13454:0.0478751575,PYIW_19970:0.1067530227):0.1352746083):0.1753960498):0.0839947725,(PYVX_18180:0.1758381036,(((HYAP_07103:0.1814790687,PHYKE_8392:0.1193275013):0.0000021667,(((PHALS_06479:0.1190170247,PHYCA_11834:0.0817747632):0.0198682131,(PITG_18455:0.0470261895,PPTG_17126:0.0549851917):0.0229069844):0.0303777364,PHYSO_321155:0.0450044334):0.0162771333):0.0692044436,PHYRA_95903:0.0331524874):0.1924337053):0.1006784089):0.5632476189);

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 Log
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: 515535

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: 19 sequences with 135 amino-acid sites
Number of constant sites: 29 (= 21.4815% of all sites)
Number of invariant (constant or ambiguous constant) sites: 29 (= 21.4815% of all sites)
Number of parsimony informative sites: 88
Number of distinct site patterns: 122

ModelFinder
-----------

Best-fit model according to BIC: Q.pfam+G4

List of models sorted by BIC scores: 

Model                  LogL         AIC      w-AIC        AICc     w-AICc         BIC      w-BIC
Q.pfam+G4         -2447.000    4966.000 +    0.176    4993.184 +     0.31    5070.590 +     0.38
LG+G4             -2447.147    4966.294 +    0.152    4993.477 +    0.267    5070.884 +    0.328
Q.pfam+I+G4       -2445.510    4965.020 +    0.287    4994.009 +    0.205    5072.515 +    0.145
LG+I+G4           -2445.574    4965.148 +    0.269    4994.137 +    0.192    5072.643 +    0.136
Q.pfam+I+R2       -2446.289    4968.578 -   0.0484    4999.453 -   0.0135    5078.979 -  0.00573
LG+I+R2           -2446.545    4969.091 -   0.0374    4999.966 -   0.0104    5079.491 -  0.00443
LG+R3             -2446.753    4971.506 -   0.0112    5004.349 -  0.00117    5084.812 -  0.00031
LG+I+R3           -2445.384    4970.769 -   0.0162    5005.662 - 0.000604    5086.980 - 0.000105
LG+R2             -2452.911    4979.821 - 0.000175    5008.811 - 0.000125    5087.317 - 8.86e-05
LG+R4             -2445.776    4973.552 -  0.00402    5010.585 - 5.16e-05    5092.669 -  6.1e-06
WAG+G4            -2463.233    4998.466 - 1.57e-08    5025.650 - 2.76e-08    5103.056 - 3.39e-08
WAG+I+G4          -2461.225    4996.449 - 4.29e-08    5025.439 - 3.07e-08    5103.944 - 2.17e-08
WAG+I+R2          -2462.039    5000.078 - 6.99e-09    5030.953 - 1.95e-09    5110.479 - 8.28e-10
JTTDCMut+G4       -2471.546    5015.091 - 3.84e-12    5042.275 - 6.77e-12    5119.681 - 8.31e-12
JTT+G4            -2471.919    5015.839 - 2.64e-12    5043.022 - 4.66e-12    5120.429 - 5.72e-12
JTTDCMut+I+G4     -2469.599    5013.199 - 9.89e-12    5042.188 - 7.07e-12    5120.694 - 5.01e-12
JTT+I+G4          -2469.971    5013.942 - 6.82e-12    5042.931 - 4.88e-12    5121.437 - 3.46e-12
LG+I              -2473.113    5018.225 - 8.01e-13    5045.409 - 1.41e-12    5122.815 - 1.73e-12
JTTDCMut+I+R2     -2470.171    5016.342 - 2.06e-12    5047.217 - 5.72e-13    5126.742 - 2.43e-13
JTT+I+R2          -2470.469    5016.937 - 1.53e-12    5047.812 - 4.25e-13    5127.337 - 1.81e-13
Dayhoff+G4        -2479.070    5030.139 - 2.07e-15    5057.323 - 3.66e-15    5134.729 - 4.49e-15
DCMut+G4          -2479.262    5030.525 - 1.71e-15    5057.709 - 3.02e-15    5135.115 -  3.7e-15
Dayhoff+I+G4      -2476.947    5027.894 - 6.37e-15    5056.884 - 4.56e-15    5135.389 - 3.23e-15
DCMut+I+G4        -2477.137    5028.274 - 5.27e-15    5057.263 - 3.77e-15    5135.769 - 2.67e-15
VT+G4             -2479.737    5031.473 - 1.06e-15    5058.657 - 1.88e-15    5136.063 -  2.3e-15
VT+I+G4           -2477.759    5029.518 - 2.83e-15    5058.508 - 2.02e-15    5137.013 - 1.43e-15
Dayhoff+I+R2      -2477.788    5031.575 - 1.01e-15    5062.450 - 2.82e-16    5141.976 -  1.2e-16
DCMut+I+R2        -2477.963    5031.927 - 8.49e-16    5062.802 - 2.36e-16    5142.327 - 1.01e-16
VT+I+R2           -2478.125    5032.250 - 7.22e-16    5063.125 - 2.01e-16    5142.650 - 8.55e-17
Q.pfam+F+G4       -2454.368    5018.737 - 6.21e-13    5096.711 - 1.02e-23    5178.527 - 1.39e-24
Q.pfam+F+I+G4     -2452.493    5016.986 - 1.49e-12    5098.832 - 3.54e-24    5179.681 - 7.78e-25
LG+F+G4           -2454.969    5019.938 -  3.4e-13    5097.913 - 5.61e-24    5179.728 -  7.6e-25
LG+F+I+G4         -2452.948    5017.895 - 9.45e-13    5099.741 - 2.25e-24    5180.591 - 4.94e-25
Q.pfam+F+I+R2     -2452.601    5019.202 - 4.92e-13    5105.072 - 1.57e-25    5184.802 - 6.01e-26
LG+F+I+R2         -2453.297    5020.593 - 2.45e-13    5106.463 - 7.81e-26    5186.194 -    3e-26
Blosum62+G4       -2508.154    5088.308 - 4.85e-28    5115.492 - 8.55e-28    5192.898 - 1.05e-27
Blosum62+I+G4     -2506.787    5087.573 -    7e-28    5116.563 - 5.01e-28    5195.068 - 3.54e-28
Blosum62+I+R2     -2507.161    5090.323 - 1.77e-28    5121.198 - 4.93e-29    5200.723 -  2.1e-29
LG                -2515.606    5101.212 - 7.65e-31    5126.667 -  3.2e-30    5202.897 - 7.07e-30
PMB+G4            -2513.826    5099.652 - 1.67e-30    5126.835 - 2.94e-30    5204.242 - 3.61e-30
PMB+I+G4          -2512.225    5098.449 - 3.04e-30    5127.439 - 2.18e-30    5205.944 - 1.54e-30
Dayhoff+F+G4      -2469.654    5049.308 - 1.43e-19    5127.283 - 2.35e-30    5209.098 - 3.18e-31
DCMut+F+G4        -2469.804    5049.607 - 1.23e-19    5127.582 - 2.03e-30    5209.397 - 2.74e-31
Dayhoff+F+I+G4    -2467.468    5046.936 - 4.67e-19    5128.782 - 1.11e-30    5209.631 - 2.44e-31
DCMut+F+I+G4      -2467.615    5047.231 - 4.03e-19    5129.077 - 9.59e-31    5209.926 -  2.1e-31
PMB+I+R2          -2512.898    5101.797 - 5.71e-31    5132.672 - 1.59e-31    5212.197 - 6.76e-32
Dayhoff+F+I+R2    -2467.608    5049.216 - 1.49e-19    5135.086 - 4.76e-32    5214.816 - 1.83e-32
DCMut+F+I+R2      -2467.745    5049.490 -  1.3e-19    5135.360 - 4.15e-32    5215.090 - 1.59e-32
JTTDCMut+F+G4     -2475.252    5060.503 - 5.29e-22    5138.478 - 8.72e-33    5220.294 - 1.18e-33
JTT+F+G4          -2475.348    5060.696 -  4.8e-22    5138.671 - 7.92e-33    5220.486 - 1.07e-33
JTTDCMut+F+I+G4   -2472.920    5057.839 -    2e-21    5139.685 - 4.77e-33    5220.535 - 1.05e-33
WAG+F+G4          -2475.429    5060.859 - 4.43e-22    5138.833 -  7.3e-33    5220.649 - 9.88e-34
JTT+F+I+G4        -2472.995    5057.990 - 1.86e-21    5139.836 - 4.42e-33    5220.685 -  9.7e-34
WAG+F+I+G4        -2473.229    5058.457 - 1.47e-21    5140.304 -  3.5e-33    5221.153 - 7.68e-34
JTTDCMut+F+I+R2   -2473.247    5060.494 - 5.31e-22    5146.364 - 1.69e-34    5226.095 - 6.49e-35
JTT+F+I+R2        -2473.277    5060.554 - 5.16e-22    5146.424 - 1.64e-34    5226.155 -  6.3e-35
WAG+F+I+R2        -2473.896    5061.791 - 2.78e-22    5147.661 - 8.84e-35    5227.392 - 3.39e-35
VT+F+G4           -2488.110    5086.219 - 1.38e-27    5164.194 - 2.27e-38    5246.009 - 3.08e-39
VT+F+I+G4         -2485.796    5083.592 - 5.12e-27    5165.438 - 1.22e-38    5246.287 - 2.68e-39
VT+F+I+R2         -2485.990    5085.980 - 1.55e-27    5171.850 - 4.94e-40    5251.580 -  1.9e-40
Blosum62+F+G4     -2513.411    5136.823 - 1.42e-38    5214.797 - 2.33e-49    5296.613 - 3.16e-50
PMB+F+G4          -2514.023    5138.047 - 7.67e-39    5216.022 - 1.27e-49    5297.837 - 1.71e-50
Blosum62+F+I+G4   -2511.605    5135.211 - 3.17e-38    5217.057 - 7.54e-50    5297.906 - 1.65e-50
PMB+F+I+G4        -2512.086    5136.171 - 1.96e-38    5218.017 - 4.67e-50    5298.866 - 1.02e-50
Blosum62+F+I+R2   -2511.764    5137.528 - 9.94e-39    5223.398 - 3.17e-51    5303.129 - 1.21e-51
PMB+F+I+R2        -2512.725    5139.450 -  3.8e-39    5225.320 - 1.21e-51    5305.051 - 4.65e-52

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+G4

State frequencies: (model)

Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 1.0053

 Category  Relative_rate  Proportion
  1         0.1380         0.2500
  2         0.4783         0.2500
  3         1.0009         0.2500
  4         2.3828         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: -2446.0452 (s.e. 131.5222)
Unconstrained log-likelihood (without tree): -639.8479
Number of free parameters (#branches + #model parameters): 36
Akaike information criterion (AIC) score: 4964.0904
Corrected Akaike information criterion (AICc) score: 4991.2741
Bayesian information criterion (BIC) score: 5068.6803

Total tree length (sum of branch lengths): 4.6964
Sum of internal branch lengths: 2.6892 (57.2595% of tree length)

WARNING: 1 near-zero internal branches (<0.0074) should be treated with caution
         Such branches are denoted by '**' in the figure below

NOTE: Tree is UNROOTED although outgroup taxon 'CCA17542' is drawn at root

+--CCA17542
|
+-----CCI44820
|
|                  +------PYAP_17747
|               +--|
|               |  |       +---PYU1_G001736
|               |  |    +--|
|               |  |    |  |                     +--SPRG_06335
|               |  |    |  |                 +---|
|               |  |    |  |                 |   +--SDRG_01782
|               |  |    |  +-----------------|
|               |  |    |                    |           +--H257_06293
|               |  |    |                    +-----------|
|               |  |    |                                +---H310_09224
|               |  +----|
|               |       |  +--PYIR_13454
|               |       +--|
|               |          +--PYIW_19970
+---------------|
                |  +----PYVX_18180
                +--|
                   |          +----HYAP_07103
                   |       +**|
                   |       |  +--PHYKE_8392
                   |    +--|
                   |    |  |        +--PHALS_06479
                   |    |  |     +--|
                   |    |  |     |  +--PHYCA_11834
                   |    |  |  +--|
                   |    |  |  |  |  +--PITG_18455
                   |    |  |  |  +--|
                   |    |  |  |     +--PPTG_17126
                   |    |  +--|
                   |    |     +--PHYSO_321155
                   +----|
                        +--PHYRA_95903

Tree in newick format:

(CCA17542:0.0761441386,CCI44820:0.2135054929,((PYAP_17747:0.2594317776,((PYU1_G001736:0.1498063812,((SPRG_06335:0.0212011740,SDRG_01782:0.0477137238):0.1527800510,(H257_06293:0.0850061078,H310_09224:0.1422366964):0.4316060840):0.6298215409):0.0652865570,(PYIR_13454:0.0478751575,PYIW_19970:0.1067530227):0.1352746083):0.1753960498):0.0839947725,(PYVX_18180:0.1758381036,(((HYAP_07103:0.1814790687,PHYKE_8392:0.1193275013):0.0000021667,(((PHALS_06479:0.1190170247,PHYCA_11834:0.0817747632):0.0198682131,(PITG_18455:0.0470261895,PPTG_17126:0.0549851917):0.0229069844):0.0303777364,PHYSO_321155:0.0450044334):0.0162771333):0.0692044436,PHYRA_95903:0.0331524874):0.1924337053):0.1006784089):0.5632476189);

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+G4{1.00533}" --length 135

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 Feb 28 01:34:25 2024
Total CPU time used: 31.8816 seconds (0h:0m:31s)
Total wall-clock time used: 10.8711 seconds (0h:0m:10s)