#NEXUS 

[! ***** MODELFIT BLOCK -- MODELTEST 3.0 *****]

[The following command will calculate a NJ tree using the JC69 model of evolution]

BEGIN PAUP;
	default lscores longfmt=yes; [Workaround for scorefile problem
					See PAUP FAQ for explanation. 
					Added by Anders Gorm]
	log file= modelfit.log replace;
	DSet distance=JC objective=ME base=equal rates=equal pinv=0
	subst=all negbrlen=setzero;
	NJ showtree=no breakties=random;
End;

[!
***** BEGIN TESTING 56 MODELS OF EVOLUTION ***** ]

BEGIN PAUP;
Set criterion=like;

[!
** Model 1 of 56 * Calculating JC **]
lscores  1/ nst=1  base=equal  rates=equal  pinv=0
scorefile=model.scores replace; 
[!
** Model 2 of 56 * Calculating JC+I **]
lscores  1/ nst=1  base=equal  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 3 of 56 * Calculating JC+GÊ**]
lscores  1/ nst=1  base=equal  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 4 of 56 * Calculating JC+I+G **]
lscores  1/ nst=1  base=equal  rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 

[!
** Model 5 of 56 * Calculating F81 **]
lscores  1/ nst=1  base=est  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 6 of 56 * Calculating F81+I **]
lscores  1/ nst=1  base=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 7 of 56 * Calculating F81+G **]
lscores  1/ nst=1  base=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 8 of 56 * Calculating F81+I+G **]
lscores  1/ nst=1  base=est  rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 

[!
** Model 9 of 56 * Calculating K80 **]
lscores  1/ nst=2  base=equal  tratio=est  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 10 of 56 * Calculating K80+I **]
lscores  1/ nst=2  base=equal  tratio=est  rates=equal  pin=est
scorefile=model.scores  append; 
[!
** Model 11 of 56 * Calculating K80+G **]
lscores  1/ nst=2  base=equal  tratio=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 12 of 56 * Calculating K80+I+G **]
lscores  1/ nst=2  base=equal  tratio=est  rates=gamma  shape=est pinv=est
scorefile=model.scores  append; 
 
[!
** Model 13 of 56 * Calculating HKY **]                
lscores  1/ nst=2  base=est  tratio=est  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 14 of 56 * Calculating HKY+I **] 
lscores  1/ nst=2  base=est  tratio=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 15 of 56 * Calculating HKY+G **] 
lscores  1/ nst=2  base=est  tratio=est  rates=gamma  shape=est  pinv=0  
scorefile=model.scores  append; 
[!
** Model 16 of 56 * Calculating HKY+I+G **] 
lscores  1/ nst=2  base=est  tratio=est  rates=gamma  shape=est  pinv=est  
scorefile=model.scores  append; 

[!
** Model 17 of 56 * Calculating TrNef **]                            [a b c d e f]
lscores  1/ nst=6  base=equal  rmat=est  rclass=(a b a a e a)  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 18 of 56 * Calculating TrNef+I **] 
lscores  1/ nst=6  base=equal  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 19 of 56 * Calculating TrNef+G **] 
lscores  1/ nst=6  base=equal rmat=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 20 of 56 * Calculating TrNef+I+G **] 
lscores  1/ nst=6  base=equal  rmat=est rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 

[!
** Model 21 of 56 * Calculating TrN **] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 22 of 56 * Calculating TrN+I **] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 23 of 56 * Calculating TrN+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 24 of 56 * Calculating TrN+I+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 


[!
** Model 25 of 56 * Calculating K3P **]                              [a b c d e f]
lscores  1/ nst=6  base=equal  rmat=est  rclass=(a b c c b a)  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 26 of 56 * Calculating K3P+I **] 
lscores  1/ nst=6  base=equal  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 27 of 56 * Calculating K3P+G **] 
lscores  1/ nst=6  base=equal rmat=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 28 of 56 * Calculating K3P+I+G **] 
lscores  1/ nst=6  base=equal  rmat=est rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 


[!
** Model 29 of 56 * Calculating K3Puf **] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 30 of 56 * Calculating K3Puf+I **] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 31 of 56 * Calculating K3Puf+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 32 of 56 * Calculating K3Puf+I+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 


[!
** Model 33 of 56 * Calculating TIMef **]                            [a b c d e f]
lscores  1/ nst=6  base=equal  rmat=est  rclass=(a b c c e a)  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 34 of 56 * Calculating TIMef+I **] 
lscores  1/ nst=6  base=equal  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 35 of 56 * Calculating TIMef+G **] 
lscores  1/ nst=6  base=equal rmat=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 36 of 56 * Calculating TIMef+I+G **] 
lscores  1/ nst=6  base=equal  rmat=est rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 


[!
** Model 37 of 56 * Calculating TIM **] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 38 of 56 * Calculating TIM+I **] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 39 of 56 * Calculating TIM+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 40 of 56 * Calculating TIM+I+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 


[!
** Model 41 of 56 * Calculating TVMef **]                            [a b c d e f]
lscores  1/ nst=6  base=equal  rmat=est  rclass=(a b c d b e)  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 42 of 56 * Calculating TVMef+I **] 
lscores  1/ nst=6  base=equal  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 43 of 56 * Calculating TVMef+G **] 
lscores  1/ nst=6  base=equal rmat=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 44 of 56 * Calculating TVMef+I+G **] 
lscores  1/ nst=6  base=equal  rmat=est rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 


[!
** Model 45 of 56 * Calculating TVM **] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 46 of 56 * Calculating TVM+I **] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 47 of 56 * Calculating TVM+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est  pinv=0
scorefile=model.scores  append; 
[!
** Model 48 of 56 * Calculating TVM+I+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est  pinv=est
scorefile=model.scores  append; 


[!
** Model 49 of 56 * Calculating SYM **]                               [a b c d e f]
lscores  1/ nst=6  base=equal  rmat=est  rclass= (a b c d e f)  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 50 of 56 * Calculating SYM+I **] 
lscores  1/ nst=6  base=equal  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 51 of 56 * Calculating SYM+G **] 
lscores  1/ nst=6  base=equal  rmat=est  rates=gamma  shape=est pinv=0  
scorefile=model.scores  append; 
[!
** Model 52 of 56 * Calculating SYM+I+G **] 
lscores  1/ nst=6  base=equal  rmat=est  rates=gamma  shape=est pinv=est  
scorefile=model.scores  append; 

[!
** Model 53 of 56 * Calculating GTR **] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=0
scorefile=model.scores  append; 
[!
** Model 54 of 56 * Calculating GTR+IÊ**] 
lscores  1/ nst=6  base=est  rmat=est  rates=equal  pinv=est
scorefile=model.scores  append; 
[!
** Model 55 of 56 * Calculating GTR+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est pinv=0  
scorefile=model.scores  append; 
[!
** Model 56 of 56 * Calculating GTR+I+G **] 
lscores  1/ nst=6  base=est  rmat=est  rates=gamma  shape=est pinv=est  
scorefile=model.scores  append; 

[!
NOTE:The molecular clock hypothesis is not included in this PAUP block for reasons of
computing time. This hypothesis may be tested once we have chosen one of the above 
models, simply calculating the log likelihood score of the chosen model with the 
molecular clock enforced and comparing it with the log likelihood previously obtained 
without enforcing the molecular clock. In this case, the molecular clock is the 
null hypothesis. The number of degrees of freedom is the number of OTUs - 2]


LOG STOP;

END;

[
lscores: tree/s
nst: number of substitution types
rmat: rate matrix
base= nucleotide frequencies
rates= rate of evolution for variable sites (same 
shape= alpha parameter of the gamma distribution
pinv= proportion of invariable sites
]

[The likelihood ratio test statistic is calculated as twice the difference between 
the log likelihood scores of the two models constrasted. When the model representing
the null hypothesis is a special case of the alternate model, this statistic 
fits a chi-square distribution with a number of degrees of freedom equal to the 
number of parameters that freely vary between the two models. A detailed explanation 
of the test of the model of DNA substitution can be found in Huelsenbeck and Crandall
Annu. Rev. Ecol. Syst. 1997. 28: 437-466]

[!***  END OF MODELTEST BLOCK  ***]