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tree_MF2.iqtree
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tree_MF2.iqtree
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IQ-TREE 2.1.4-beta COVID-edition built Jun 24 2021
Input file name: all_seqs_mafft.fa
Type of analysis: ModelFinder + tree reconstruction
Random seed number: 51880
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: 103 sequences with 6727 nucleotide sites
Number of constant sites: 1838 (= 27.3227% of all sites)
Number of invariant (constant or ambiguous constant) sites: 1838 (= 27.3227% of all sites)
Number of parsimony informative sites: 4543
Number of distinct site patterns: 5018
ModelFinder
-----------
Best-fit model according to BIC: GTR+F+I+G4
List of models sorted by BIC scores:
Model LogL AIC w-AIC AICc w-AICc BIC w-BIC
GTR+F+I+G4 -209288.601 419003.202 - 0.00514 419017.199 - 0.0154 420454.559 + 1
GTR+F+R10 -209267.335 418992.670 + 0.995 419008.884 + 0.985 420553.050 - 4.1e-22
GTR+F+R9 -209314.589 419083.179 - 2.21e-20 419099.106 - 2.52e-20 420629.931 - 8.29e-39
GTR+F+R8 -209440.416 419330.831 - 3.69e-74 419346.475 - 4.86e-74 420863.955 - 1.26e-89
TIM3+F+I+G4 -209646.315 419714.631 - 1.68e-157 419728.363 - 5.76e-157 421152.360 - 2.98e-152
GTR+F+R7 -209622.769 419691.537 - 1.74e-152 419706.900 - 2.64e-152 421211.033 - 5.42e-165
GTR+F+G4 -209777.787 419979.573 - 4.95e-215 419993.438 - 1.59e-214 421424.117 - 2.91e-211
GTR+F+R6 -209895.530 420233.060 - 4.47e-270 420248.144 - 7.79e-270 421738.928 - 1.27e-279
TVM+F+I+G4 -209998.757 420421.514 - 5.35e-311 420435.378 - 1.71e-310 421866.058 - 3.14e-307
TIM2+F+I+G4 -210026.424 420474.848 - 1.43e-322 420488.580 - 4.79e-322 421912.577 - 2.48e-317
TPM3u+F+I+G4 -210242.041 420904.082 - 0 420917.683 - 0 422334.998 - 0
TPM3+F+I+G4 -210242.041 420904.082 - 0 420917.683 - 0 422334.998 - 0
GTR+F+R5 -210300.929 421039.857 - 0 421054.666 - 0 422532.098 - 0
TN+F+I+G4 -210411.138 421242.277 - 0 421255.877 - 0 422673.192 - 0
TIM+F+I+G4 -210406.862 421235.725 - 0 421249.457 - 0 422673.455 - 0
TPM2u+F+I+G4 -210554.489 421528.978 - 0 421542.579 - 0 422959.894 - 0
TPM2+F+I+G4 -210554.489 421528.978 - 0 421542.579 - 0 422959.894 - 0
K3Pu+F+I+G4 -210826.113 422072.226 - 0 422085.827 - 0 423503.142 - 0
HKY+F+I+G4 -210841.155 422100.311 - 0 422113.780 - 0 423524.412 - 0
GTR+F+R4 -210911.826 422257.652 - 0 422272.187 - 0 423736.265 - 0
GTR+F+R3 -212162.830 424755.661 - 0 424769.926 - 0 426220.646 - 0
SYM+I+G4 -213226.732 426873.463 - 0 426887.064 - 0 428304.379 - 0
TVMe+I+G4 -213281.894 426981.789 - 0 426995.258 - 0 428405.891 - 0
TIM2e+I+G4 -213663.830 427743.660 - 0 427756.999 - 0 429160.948 - 0
TIMe+I+G4 -214363.014 429142.027 - 0 429155.366 - 0 430559.315 - 0
K3P+I+G4 -214459.589 429333.178 - 0 429346.387 - 0 430743.652 - 0
TIM3e+I+G4 -214832.923 430081.847 - 0 430095.186 - 0 431499.135 - 0
TNe+I+G4 -214951.885 430317.771 - 0 430330.980 - 0 431728.245 - 0
K2P+I+G4 -215057.173 430526.346 - 0 430539.426 - 0 431930.006 - 0
GTR+F+R2 -216405.979 433237.958 - 0 433251.955 - 0 434689.315 - 0
F81+F+I+G4 -218276.618 436969.236 - 0 436982.575 - 0 438386.524 - 0
JC+I+G4 -219643.022 439696.045 - 0 439708.997 - 0 441092.891 - 0
GTR+F+I -224461.339 449346.677 - 0 449360.541 - 0 450791.221 - 0
GTR+F -241768.777 483959.554 - 0 483973.286 - 0 485397.284 - 0
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: GTR+F+I+G4
Rate parameter R:
A-C: 7.8030
A-G: 10.6540
A-T: 2.3108
C-G: 3.9080
C-T: 25.4819
G-T: 1.0000
State frequencies: (empirical counts from alignment)
pi(A) = 0.3329
pi(C) = 0.1534
pi(G) = 0.2096
pi(T) = 0.3041
Rate matrix Q:
A -0.7505 0.2173 0.4056 0.1276
C 0.4717 -2.028 0.1488 1.407
G 0.644 0.1088 -0.808 0.05522
T 0.1397 0.7096 0.03807 -0.8873
Model of rate heterogeneity: Invar+Gamma with 4 categories
Proportion of invariable sites: 0.2335
Gamma shape alpha: 0.6353
Category Relative_rate Proportion
0 0 0.2335
1 0.07886 0.1916
2 0.4322 0.1916
3 1.172 0.1916
4 3.535 0.1916
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: -209267.2469 (s.e. 2041.7676)
Unconstrained log-likelihood (without tree): -52874.5086
Number of free parameters (#branches + #model parameters): 213
Akaike information criterion (AIC) score: 418960.4938
Corrected Akaike information criterion (AICc) score: 418974.4910
Bayesian information criterion (BIC) score: 420411.8512
Total tree length (sum of branch lengths): 34.1049
Sum of internal branch lengths: 12.6038 (36.9559% of tree length)
WARNING: 2 near-zero internal branches (<0.0001) should be treated with caution
Such branches are denoted by '**' in the figure below
NOTE: Tree is UNROOTED although outgroup taxon 'AB620030.1' is drawn at root
+--AB620030.1
|
| +-------AB620102.1
| +--|
| | +------AB620105.1
| +--|
| | | +--ON571586.1
| | +-------|
| | +**ON571589.1
| +--|
| | | +-------AF005729.1
| | | +--|
| | | | +--------NC_043407.1
| | | +--|
| | | | +---MN850095.1
| | | +--|
| | | | +------EU788002.1
| | | +--|
| | | | +-------GQ200821.1
| | +--|
| | | +----FJ858378.1
| | +---|
| | | +----GU997097.1
| | +--|
| | +---NC_038299.1
| +--|
| | | +----AB677488.1
| | | +--|
| | | | +-----JX028271.1
| | | +--|
| | | | +----MN639746.1
| | | +---|
| | | | | +--HQ728461.1
| | | | | +--|
| | | | | | +--MT993951.1
| | | | | +---|
| | | | | | +--KU297981.1
| | | | | +--|
| | | | | | | +--KY751731.1
| | | | | | | +--|
| | | | | | | | +--MK883761.1
| | | | | | | +--|
| | | | | | | | +---MK542664.1
| | | | | | +--|
| | | | | | +---MT441741.1
| | | | | +--|
| | | | | | +-----KJ857315.1
| | | | +--|
| | | | +-----KJ857316.1
| | +--|
| | +---------KT899703.1
| +-----|
| | +------------HM015222.1
| +---|
| | | +--EF641806.1
| | | +--|
| | | | +--KX779125.1
| | | +------|
| | | | +--EF641807.1
| | | +----|
| | | | +--------EU001330.1
| | | +----------|
| | | | | +--------------JX193697.1
| | | | +--|
| | | | +---------JX193700.1
| | +-----|
| | | +-----EU424341.1
| | | +-----------|
| | | | +---NC_078485.1
| | | +-------|
| | | | +-----------JX990965.1
| | | +--|
| | | | | +--FJ593498.1
| | | | | +--|
| | | | | | | +--KF010517.1
| | | | | | +--|
| | | | | | +---KF031355.1
| | | | | +--|
| | | | | | +--KX512432.1
| | | | | +-----|
| | | | | | | +--JX990946.1
| | | | | | +--|
| | | | | | +--KR072623.1
| | | | +------------|
| | | | +---KY040508.1
| | | +--|
| | | | | +-------------JN037851.1
| | | | | +--|
| | | | | | +-------KT316176.1
| | | | | +--|
| | | | | | | +--JX912953.2
| | | | | | | +--|
| | | | | | | | +--KF704713.1
| | | | | | +-----|
| | | | | | | +--KF704715.1
| | | | | | | +---|
| | | | | | | | | +--KF704716.1
| | | | | | | | +--|
| | | | | | | | +--KF704717.1
| | | | | | +--|
| | | | | | +--NC_078262.1
| | | | +----|
| | | | | +**KM102249.1
| | | | | +----|
| | | | | | +**NC_038515.1
| | | | | +--|
| | | | | | +----MN337866.1
| | | | +--|
| | | | +----------MG663536.1
| | | +--|
| | | | | +-----------JX465369.1
| | | | | +--|
| | | | | | +-----------OR684449.1
| | | | +--|
| | | | | +**KU950715.1
| | | | | +------------|
| | | | | | +**NC_034401.1
| | | | +----|
| | | | | +**MK165653.1
| | | | +-----------|
| | | | +**NC_055632.1
| | +--|
| | | +**JQ287716.2
| | | +--------|
| | | | +**KJ000540.1
| | +----|
| | | +**JX465379.1
| | | +-------|
| | | | | +--JX465381.1
| | | | | +--|
| | | | | | +--JX465382.1
| | | | +--|
| | | | +**JX465383.1
| | +---|
| | | +**KR920360.1
| | +--------|
| | | +--KX845680.1
| | | +**|
| | | | | +--OM912843.1
| | | | +--|
| | | | | +**OM912844.1
| | | | +**|
| | | | +**OM963009.1
| | | +--|
| | | | | +**OM912840.1
| | | | +--|
| | | | +**OM912842.1
| | | +--|
| | | | | +--OR934973.1
| | | | +--|
| | | | +--OR934974.1
| | +--|
| | +--OM912841.1
| +----|
| | | +---------EF050454.1
| | | +--|
| | | | +------KC631784.1
| | | +---|
| | | | +---------HQ834697.1
| | | +--|
| | | | | +-------EU929078.1
| | | | | +--|
| | | | | | | +---GU566021.1
| | | | | | | +--|
| | | | | | | | +----KC880348.1
| | | | | | +--|
| | | | | | | +----JX990941.1
| | | | | | | +--|
| | | | | | | | +----KF974361.1
| | | | | | +--|
| | | | | | +-----KJ857320.1
| | | | | +--|
| | | | | | | +-----KF705679.1
| | | | | | +--|
| | | | | | +------MN006903.1
| | | | +--|
| | | | +-----------NC_043175.1
| | +--|
| | +--------------MF683846.1
| +--|
| | | +--AM998806.1
| | | +--|
| | | | | +----KC490923.1
| | | | +--|
| | | | +----LC553715.1
| | +--|
| | | +--GU904045.1
| | | +--|
| | | | +--MK605664.1
| | +---|
| | +--MK605665.1
| +--|
| | | +------DQ268652.1
| | +--|
| | | +--MG386252.1
| | +-----|
| | +--OR047284.1
+--|
| | +--MN608087.1
| +--|
| | +--MW349026.1
| +---|
| +--MZ191082.1
|
+--AY675354.1
Tree in newick format:
(AB620030.1:0.0770995939,((((((((((AB620102.1:0.3588065046,AB620105.1:0.3165473652):0.0821586849,(ON571586.1:0.0003515120,ON571589.1:0.0000010012):0.3527400811):0.0680023543,(((((AF005729.1:0.3759335127,NC_043407.1:0.3954963563):0.0611311185,MN850095.1:0.2116065200):0.1127115374,EU788002.1:0.3286792642):0.0815975707,GQ200821.1:0.3674148748):0.0440828589,(FJ858378.1:0.2199499085,(GU997097.1:0.2425164197,NC_038299.1:0.2144221815):0.0646573090):0.1905912138):0.0596436320):0.1484172803,((((AB677488.1:0.2316506202,JX028271.1:0.2948111929):0.0621368110,MN639746.1:0.2298792944):0.1005088418,(((((HQ728461.1:0.0991567136,MT993951.1:0.1198842762):0.0800845748,KU297981.1:0.1619032514):0.1912997763,(((KY751731.1:0.1151675633,MK883761.1:0.1215513133):0.0991292136,MK542664.1:0.1987388552):0.0574424807,MT441741.1:0.1900166819):0.0617581973):0.0859008638,KJ857315.1:0.2792052513):0.0473721222,KJ857316.1:0.2726854054):0.0543095293):0.1993519947,KT899703.1:0.4702641608):0.1130427354):0.0567583322,HM015222.1:0.6085533897):0.2678509622,(((((EF641806.1:0.0146130428,KX779125.1:0.0138813015):0.0769933956,EF641807.1:0.0804304886):0.3348018402,EU001330.1:0.4229637956):0.2537600151,(JX193697.1:0.6694651952,JX193700.1:0.4768295223):0.1299118644):0.4856189640,((((((EU424341.1:0.2655736301,NC_078485.1:0.2155737705):0.5584031498,JX990965.1:0.5365716480):0.3825615241,((((FJ593498.1:0.1138363785,(KF010517.1:0.1090738155,KF031355.1:0.1938532274):0.0302352730):0.0252829599,KX512432.1:0.1341353029):0.0562176664,(JX990946.1:0.0340586322,KR072623.1:0.0079225353):0.0731929722):0.2867950074,KY040508.1:0.2040549175):0.5710714330):0.0917365691,(((JN037851.1:0.6363596205,KT316176.1:0.3813258859):0.0457202961,((JX912953.2:0.1408205533,KF704713.1:0.1621042435):0.1151187740,((KF704715.1:0.0038419143,(KF704716.1:0.0062926056,KF704717.1:0.0145827984):0.0188872992):0.1803185544,NC_078262.1:0.1753221884):0.0585001619):0.2696827726):0.0552003457,(((KM102249.1:0.0000010012,NC_038515.1:0.0000010012):0.2418622517,MN337866.1:0.2548792506):0.1428206855,MG663536.1:0.4935038761):0.0875187883):0.2338708103):0.0683902968,((JX465369.1:0.5394460161,OR684449.1:0.5549790744):0.1176676295,((KU950715.1:0.0000010012,NC_034401.1:0.0000010012):0.5735128675,(MK165653.1:0.0000010012,NC_055632.1:0.0000010012):0.5310778690):0.2608252151):0.0898363484):0.0764726404,((JQ287716.2:0.0000021074,KJ000540.1:0.0000010012):0.4268860265,((JX465379.1:0.0000021982,((JX465381.1:0.0038140079,JX465382.1:0.0077280594):0.0196553954,JX465383.1:0.0000029366):0.0077412184):0.3703389759,(KR920360.1:0.0000026153,((((KX845680.1:0.0037977008,(OM912843.1:0.0137478426,(OM912844.1:0.0000010012,OM963009.1:0.0000010012):0.0000026467):0.0033915957):0.0000023045,(OM912840.1:0.0000010012,OM912842.1:0.0000026231):0.0134326942):0.0542319550,(OR934973.1:0.0049495147,OR934974.1:0.0163538057):0.0197507421):0.0236899768,OM912841.1:0.0180641874):0.0207275712):0.4174804472):0.1916462760):0.2447897682):0.1261036705):0.2959003464):0.2133130839,((((EF050454.1:0.4628125970,KC631784.1:0.3153514327):0.1190054783,HQ834697.1:0.4505636711):0.1998234265,(((EU929078.1:0.3652508563,((GU566021.1:0.2054838091,KC880348.1:0.2583788398):0.0478872193,((JX990941.1:0.2461762360,KF974361.1:0.2325006783):0.0505542087,KJ857320.1:0.2845112353):0.0578580037):0.0883686862):0.0719530889,(KF705679.1:0.2889759622,MN006903.1:0.3471734474):0.0840083434):0.0520240054,NC_043175.1:0.5411542222):0.0713251183):0.0953236301,MF683846.1:0.6820457223):0.0500406347):0.2568787361,((AM998806.1:0.1470115049,(KC490923.1:0.2430122771,LC553715.1:0.2435859606):0.0475189219):0.1384966560,((GU904045.1:0.0902094432,MK605664.1:0.1225434879):0.0605979815,MK605665.1:0.0399370545):0.2022568948):0.0690722462):0.0190824385,(DQ268652.1:0.3467568179,(MG386252.1:0.0136830121,OR047284.1:0.0549142457):0.2848732388):0.0911513051):0.1717011089,(MN608087.1:0.1744086219,(MW349026.1:0.0248683399,MZ191082.1:0.0110718887):0.1996770465):0.0405038034):0.1049204770,AY675354.1:0.0948983427);
TIME STAMP
----------
Date and time: Sat Apr 20 14:46:58 2024
Total CPU time used: 2009.97 seconds (0h:33m:29s)
Total wall-clock time used: 300.651 seconds (0h:5m:0s)