PAUP Nexus file- advanced.

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#NEXUS

[ LOG  FILE = ex.10nov.log append;]

Begin data;
Dimensions ntax=7 nchar=100;

Format missing=? Gap=- interleave datatype=DNA;
matrix

     AYA  ATGCATGTCTAAGTATAAGT AA--TTATACGGCGAAACTG CGAATGGCTCATTATATAAC TTATCG?TTATTTGATAATA C-TTTACTACTTGG-ATAAC
     BAB  ATGCATGTCTAAGTATAAGT AA-TTTATACAGTGAAACTC CGAATGGCTCATTAAATCAC TTATCGTTTATTTGATAGTT CCTTTACTACATGGTATAAC
     COC  ATGCATGTCTAAGTATAAGC AA-TCTATACAGTGAAACTG CGAATGGCTC?TTAAATCAG TTATCGTTTATTTGATAGTA CCTT-CCTACTTGG-ATAAC
     DCD  ATGAATGTCTAAGTATAAGC AA-TCTWTACGGTGAAACTG CGAATGGCTCATTATATCAG TTATCGTTTATTTGATAGTA CCTT-ACTACTTGG-ATA-C
     FLT  ATGCATGTCTAAGTATAAGT AA--TTATACCGTGAAACTG CGAATGGCTCATTAAATCAC TTATCGTTTATTTGATAATA CCTT-ACTACTTGG-ATAAC
     GNC  ATGCATGTCTAAGTATAAGT AA-TTTGTACGGTGAAACTC CGAATGGCTCATTAAATCAC TTATCGTTTATTTGATAGTA CCTT-ACTACATGG-ATACC
     IEU  ATGCAAGTCTAAGTTTAAGT AC--CTAAACGGCGAAACTG CGAATGGCTCATTAAATCAG TTATCGTATATTTGATAGTA CCTA--CTACATGG-ATAAC
;

END;

SET Tcompress=Yes increase=auto noerrorstop nowarnreset autoclose=yes [maxtrees=5000 increase=no root=midpoint] ;

begin paup;
charset ovisst=24 30-35;
exclude ovisst;
taxset Ixodes = 1 2 3;
outgroup 3;
endblock;

delete Ixodes;
	[] 
  

set crit=parsimony;  
        hsearch  ADDSEQ = RANDOM NREPS = 40 ;  [BANdb  branch and bound search ] 
[		describe all/ Tcompress=Yes PLOT =PHYLOGRAM ;
	[	SAVETREES BRLENS FILE = ex.1nov.tree.pars;    ]
	    CONTREE / strict MAJRULE  LE50 NOGRPFREQ;
]		
BOOTSTRAP NReps=1000 SE= [Heuristic Bandb Nj ] Fast   NOshow=30 [/ ADDSEQ = simple [option for heuristic search]];

		
SET CRITERION=distance;
  dset distance=hky85   [p jc k2p hky85]; 		
	nj ;
SAVETREES BRLENS FILE = ex.24oct.hky.nj.tree;
	SHOWDIST;

SET CRITERION=Likelihood;
 GETTREES FILE= ex.24oct.hky.nj.tree  [Storebrlens=Yes unrooted=yes ]  MODE=7 [3 will overwrite any trees in memory];
 
  LIKELIHOODS 1 / TRATIO=ESTIMATE shape=estimate RATES=gamma PINVAR=E V=hky NC=4 [3] C=n ;
       LSET TRATIO=PREVIOUS shape=PREVIOUS PINVAR=PREVIOUS;

        hsearch  STARt=Current  [SWAP = { TBR | SPR | NNI | NONE }  note- this is a 
						persistent option, use the default tbr for most searches, 
						nearest neighbor interchange for quick searches];
		SAVETREES BRLENS FILE = ex.1nov.ml.tree; 
	    describe all /Tcompress=Yes PLOT =PHYLOGRAM  ;
gammaplot shape=previous;
SHOWMATRIX  Showexcluded=Yes CMCStatus=Yes ;


[The sets below divides the data into first, second and third positions, for amino acid coding DNA]

   BEGIN SETS;
      CHARSET 1st =1-100\3;
      CHARSET 2nd =2-100\3;
      CHARSET 3rd =3-100\3;
	  
   END;

[CHARPARTITION uses the sets made above to partition the data, 
for estimating or setting parameters separately for the three coding positions]

 CHARPARTITION codons = 1stpos:1st, 2ndpos:2nd, 3rdpos:3rd[,
         noncoding:REMAINDER];  
		 
		
[The commands below should test the molecular clock when the 
topologies of the clock constrained and unconstrained trees are different.  
This is a very strict test.  You should use the log likelihood 
ratio test if you can (See PHYLIP DNAMLK documentation). ]

delete   BAB COC DCD/ clear ;  [! delete BAB COC DCD]	  

 SET CRITERION=distance; 
  dset di=hky85  	[di=k2p];	
nj ;
root; 

SET CRITERION=Likelihood; 
	  LSET C=Y ;  
LIKELIHOODS 1 / TRATIO=Estimate RATES=sites SITERATES=PARTITION:codons [shape=estimate]  V=hky NC=3 C=Y ;
       LSET TRATIO=previous  RATES=SITES SITERATES=previous  c=y; 
        hsearch  STARt=Current ;
		        SAVETREES BRLENS FILE = no.29oct.nodougcrisnakip.tree; 
		
	    describe all /Tcompress=Yes PLOT =PHYLOGRAM ;   
		gammaplot ;	


	LSET C=N;
	deroot;	
LSET  USERbrlens=yes;
		        SAVETREES BRLENS  FILE = ex.clock.test.trees;
LSET  USERbrlens=no;	
	        	SAVETREES BRLENS append FILE = ex.clock.test.trees;
				
[! At this point one must take  the treefile 'ex.clock.test.trees' and merge the two separate
treefiles within it into one treefile with two trees- sounds worse than it is.  
Then run the file with the commands below]


delete   BAB COC DCD/ clear ;  [! delete    BAB COC DCD]	

GETTREES FILE= ex.clock.test.trees Storebrlens=Yes unrooted=yes ;

SET CRITERION=Likelihood; 
LIKELIHOODS 1 / USERbrlens=yes TRATIO=Estimate RATES=sites SITERATES=PARTITION:codons [shape=estimate]  V=hky NC=3 C=n ;
       LSET TRATIO=previous  RATES=SITES SITERATES=previous ;
Likelihood all /KH  USERbrlens=yes;  
	    describe all /Tcompress=Yes PLOT =PHYLOGRAM ; 
Likelihood all /KH USERbrlens=no;	[This should give two trees of exactly the same log likelihood]

log stop;
[leave;]
quit;