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lasv-l_matched_sle.iqtree
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IQ-TREE 1.6.5 built May 8 2018
Input file name: lasv-l_matched_sle.mafft.fasta
Type of analysis: tree reconstruction
Random seed number: 266671
REFERENCES
----------
To cite IQ-TREE please use:
Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh
(2015) IQ-TREE: A fast and effective stochastic algorithm for estimating
maximum likelihood phylogenies. Mol Biol Evol, 32:268-274.
https://doi.org/10.1093/molbev/msu300
SEQUENCE ALIGNMENT
------------------
Input data: 72 sequences with 7430 nucleotide sites
Number of constant sites: 4030 (= 54.2396% of all sites)
Number of invariant (constant or ambiguous constant) sites: 4030 (= 54.2396% of all sites)
Number of parsimony informative sites: 2887
Number of distinct site patterns: 3314
SUBSTITUTION PROCESS
--------------------
Model of substitution: GTR+F+G4
Rate parameter R:
A-C: 0.6225
A-G: 33.5310
A-T: 1.8858
C-G: 0.7512
C-T: 24.6675
G-T: 1.0000
State frequencies: (empirical counts from alignment)
pi(A) = 0.289
pi(C) = 0.2368
pi(G) = 0.1737
pi(T) = 0.3005
Rate matrix Q:
A -0.877 0.01977 0.7813 0.076
C 0.02413 -1.036 0.0175 0.9941
G 1.3 0.02386 -1.364 0.0403
T 0.07309 0.7834 0.0233 -0.8798
Model of rate heterogeneity: Gamma with 4 categories
Gamma shape alpha: 0.2981
Category Relative_rate Proportion
1 0.005145 0.25
2 0.103 0.25
3 0.5927 0.25
4 3.299 0.25
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: -69932.9177 (s.e. 844.4116)
Unconstrained log-likelihood (without tree): -41136.5617
Number of free parameters (#branches + #model parameters): 150
Akaike information criterion (AIC) score: 140165.8353
Corrected Akaike information criterion (AICc) score: 140172.0587
Bayesian information criterion (BIC) score: 141202.8275
Total tree length (sum of branch lengths): 1.8686
Sum of internal branch lengths: 0.6186 (33.1039% of tree length)
WARNING: 1 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 'G502-L-SLE-2009' is drawn at root
+----G502-L-SLE-2009
|
+----G1180-L-SLE-2010
|
| +-----G503-L-SLE-2009
| +--|
| | | +--G610-L-SLE-2009
| | | +--|
| | | | | +--G693-L-SLE-2009
| | | | +--|
| | | | +--G771-L-SLE-2010
| | | +--|
| | | | | +--G1792-L-SLE-2011
| | | | | +--|
| | | | | | +--G2565-L-SLE-2012
| | | | +--|
| | | | +--G1960-L-SLE-2011
| | | +--|
| | | | +---G2197-L-SLE-2011
| | | +---|
| | | | +---LM032-L-SLE-2010
| | | +--|
| | | | | +--G1959-L-SLE-2011
| | | | +------|
| | | | +--G3010-L-SLE-2012
| | | +--|
| | | | | +--G636-L-SLE-2009
| | | | | +--|
| | | | | | +--G2315-L-SLE-2012
| | | | | +--|
| | | | | | +--G2903-L-SLE-2012
| | | | | +--|
| | | | | | +---G3206-L-SLE-2012
| | | | | +--|
| | | | | | | +--G676-L-SLE-2009
| | | | | | | +---|
| | | | | | | | +--G2405-L-SLE-2012
| | | | | | | +--|
| | | | | | | | | +--G1647-L-SLE-2011
| | | | | | | | +--|
| | | | | | | | | +--G2295-L-SLE-2012
| | | | | | | | +--|
| | | | | | | | +--G2587-L-SLE-2012
| | | | | | | +--|
| | | | | | | | | +--G1190-L-SLE-2010
| | | | | | | | | +--|
| | | | | | | | | | +--G2944-L-SLE-2012
| | | | | | | | | +--|
| | | | | | | | | | +--LM765-L-SLE-2012
| | | | | | | | | +--|
| | | | | | | | | | | +--G1727-L-SLE-2011
| | | | | | | | | | +--|
| | | | | | | | | | +--G3148-L-SLE-2012
| | | | | | | | | +--|
| | | | | | | | | | | +--Z0947-L-SLE-2011
| | | | | | | | | | +--|
| | | | | | | | | | +--Z0948-L-SLE-2011
| | | | | | | | +--|
| | | | | | | | | +--G2280-L-SLE-2012
| | | | | | | | | +--|
| | | | | | | | | | +--G2612-L-SLE-2012
| | | | | | | | +--|
| | | | | | | | | +**G3016-L-SLE-2012
| | | | | | | | +--|
| | | | | | | | +**G3106-L-SLE-2012
| | | | | | | +--|
| | | | | | | | +-----G692-L-SLE-2009
| | | | | | +--|
| | | | | | | +--G1774-L-SLE-2011
| | | | | | | +--|
| | | | | | | | +--G2222-L-SLE-2011
| | | | | | +--|
| | | | | | +--LM395-L-SLE-2009
| | | | | +--|
| | | | | | +--Josiah-L-SLE-1976
| | | | | +--|
| | | | | | | +------G2868-L-SLE-2012
| | | | | | +--|
| | | | | | +------G808-L-SLE-2010
| | | | +--|
| | | | | +-----G733-L-SLE-2010
| | | | | +--|
| | | | | | +-----G2554-L-SLE-2012
| | | | | +----|
| | | | | | | +--G1618-L-SLE-2011
| | | | | | +---|
| | | | | | +--G1646-L-SLE-2011
| | | | | +--|
| | | | | | | +--G2392-L-SLE-2012
| | | | | | | +----|
| | | | | | | | | +--G3229-L-SLE-2012
| | | | | | | | +--|
| | | | | | | | | +**G3151-L-SLE-2012
| | | | | | | | | +**|
| | | | | | | | | | +**G3248-L-SLE-2012
| | | | | | | | +--|
| | | | | | | | +**G3170-L-SLE-2012
| | | | | | +----|
| | | | | | +--------G2427-L-SLE-2012
| | | | | +--|
| | | | | | +------------NL-L-SLE-2000
| | | | +--|
| | | | | +-------------G2263-L-SLE-2012
| | | | +--|
| | | | | +--G1529-L-SLE-2011
| | | | | +-------------|
| | | | | | +--G3234-L-SLE-2012
| | | | | +--|
| | | | | | | +--G2259-L-SLE-2012
| | | | | | | +--|
| | | | | | | | | +--G2723-L-SLE-2012
| | | | | | | | +--|
| | | | | | | | +--G3278-L-SLE-2012
| | | | | | | +--|
| | | | | | | | +--G2557-L-SLE-2012
| | | | | | +---------------|
| | | | | | +--G2615-L-SLE-2012
| | | | | +---|
| | | | | | +---------------------G2363-L-SLE-2012
| | | | | +--|
| | | | | | +------------------------G2431-L-SLE-2012
| | | | | +--|
| | | | | | +-----------------------G2141-L-SLE-2011
| | | | +------------|
| | | | +-----------------------------------G1442-L-SLE-2011
| | +--|
| | | +--G2165-L-SLE-2011
| | | +--|
| | | | | +--G2184-L-SLE-2011
| | | | +--|
| | | | | +--LM776-L-SLE-2012
| | | | +--|
| | | | +--LM774-L-SLE-2012
| | | +------|
| | | | | +--LM222-L-SLE-2010
| | | | +--|
| | | | +--LM778-L-SLE-2012
| | +--|
| | +---------G2318-L-SLE-2012
+--|
| +-----LM779-L-SLE-2012
+--|
+------G2147-L-SLE-2011
Tree in newick format:
(G502-L-SLE-2009:0.0225824764,G1180-L-SLE-2010:0.0211369958,((G503-L-SLE-2009:0.0243011475,(((((((G610-L-SLE-2009:0.0017104951,(G693-L-SLE-2009:0.0004815226,G771-L-SLE-2010:0.0004817320):0.0003459648):0.0031328380,((G1792-L-SLE-2011:0.0007307798,G2565-L-SLE-2012:0.0018245955):0.0004815978,G1960-L-SLE-2011:0.0005204541):0.0043739959):0.0148426581,G2197-L-SLE-2011:0.0185259424):0.0015414854,LM032-L-SLE-2010:0.0178395068):0.0170261513,(G1959-L-SLE-2011:0.0111367495,G3010-L-SLE-2012:0.0134092923):0.0278845887):0.0004511672,(((((((G636-L-SLE-2009:0.0009210472,G2315-L-SLE-2012:0.0039575748):0.0078722802,G2903-L-SLE-2012:0.0125043717):0.0093192256,G3206-L-SLE-2012:0.0182490944):0.0152834104,(((((G676-L-SLE-2009:0.0027027159,G2405-L-SLE-2012:0.0024203630):0.0166935066,(G1647-L-SLE-2011:0.0132787973,(G2295-L-SLE-2012:0.0003647077,G2587-L-SLE-2012:0.0004782335):0.0106166333):0.0062733023):0.0008410762,(((((G1190-L-SLE-2010:0.0018239947,G2944-L-SLE-2012:0.0050674337):0.0044341665,LM765-L-SLE-2012:0.0076397194):0.0009827071,(G1727-L-SLE-2011:0.0081783696,G3148-L-SLE-2012:0.0089172238):0.0011793005):0.0014860545,(Z0947-L-SLE-2011:0.0023570328,Z0948-L-SLE-2011:0.0006729426):0.0073506040):0.0106221376,((G2280-L-SLE-2012:0.0093119824,G2612-L-SLE-2012:0.0075209969):0.0015693085,(G3016-L-SLE-2012:0.0000020438,G3106-L-SLE-2012:0.0000020438):0.0092870123):0.0108097981):0.0004933142):0.0036877367,G692-L-SLE-2009:0.0238359392):0.0006811990,((G1774-L-SLE-2011:0.0051553511,G2222-L-SLE-2011:0.0067477449):0.0071352757,LM395-L-SLE-2009:0.0132171941):0.0089236851):0.0103741447):0.0008512177,Josiah-L-SLE-1976:0.0084807391):0.0002252329,(G2868-L-SLE-2012:0.0280376029,G808-L-SLE-2010:0.0297880518):0.0085980439):0.0084266887,(((((G733-L-SLE-2010:0.0261275187,G2554-L-SLE-2012:0.0252168503):0.0019895781,(G1618-L-SLE-2011:0.0064361107,G1646-L-SLE-2011:0.0053456137):0.0169895924):0.0216611983,((G2392-L-SLE-2012:0.0066717507,(G3229-L-SLE-2012:0.0070113785,((G3151-L-SLE-2012:0.0000020438,G3248-L-SLE-2012:0.0000020438):0.0000020438,G3170-L-SLE-2012:0.0000020438):0.0088786744):0.0006514378):0.0225859597,G2427-L-SLE-2012:0.0374507793):0.0217287539):0.0052009820,NL-L-SLE-2000:0.0515337230):0.0031111567,(G2263-L-SLE-2012:0.0570396096,((((((G1529-L-SLE-2011:0.0129210796,G3234-L-SLE-2012:0.0114546487):0.0558101226,(((G2259-L-SLE-2012:0.0124046454,(G2723-L-SLE-2012:0.0105123717,G3278-L-SLE-2012:0.0111047622):0.0019284244):0.0008711950,G2557-L-SLE-2012:0.0133532004):0.0019222491,G2615-L-SLE-2012:0.0129351478):0.0656052789):0.0087509993,G2363-L-SLE-2012:0.0884908496):0.0175483382,G2431-L-SLE-2012:0.0993572143):0.0062763887,G2141-L-SLE-2011:0.0959796379):0.0073934873,G1442-L-SLE-2011:0.1419783552):0.0543075193):0.0051848589):0.0090125587):0.0046385563):0.0028511986,(((G2165-L-SLE-2011:0.0107666645,(G2184-L-SLE-2011:0.0094865368,(LM776-L-SLE-2012:0.0050271210,LM774-L-SLE-2012:0.0061620925):0.0019193782):0.0049643807):0.0003148939,(LM222-L-SLE-2010:0.0067001347,LM778-L-SLE-2012:0.0104832339):0.0031301769):0.0290223648,G2318-L-SLE-2012:0.0401611937):0.0007842184):0.0099183898):0.0036031575,(LM779-L-SLE-2012:0.0248373958,G2147-L-SLE-2011:0.0285505913):0.0004642322):0.0036122297);
TIME STAMP
----------
Date and time: Tue Aug 14 10:29:50 2018
Total CPU time used: 159.631 seconds (0h:2m:39s)
Total wall-clock time used: 77.3744 seconds (0h:1m:17s)