#NEXUS

BEGIN DATA;
	DIMENSIONS  NTAX=23 NCHAR=172;
	FORMAT DATATYPE = DNA GAP = - MISSING = ?;
	MATRIX
	AF050522.1_T_cruzi_M6241                                     TGTACACAGGCCCCGGTACCCGCGAACAACCCCTCATAAAAATGCGATTTTTGTACACAGGCCCGGGAACCGCGAACAACCCCTCATCAAATTTGAAAACGGTC-CGGGGCCAGGAACTTTTTCAACTAACGCTATTATTGATAAAAACAGTTTCTGTACTATATTGGTACG
	JX154671.1_T_cruzi_Dn43                                      TGTACACAGGCCCCGGTACCCGCSAACAACCCCTCATAAAAATGCGATTTTTGTACACAGGCCCGGGAACCGCGAACAACCCCTCATCAAATTTGAAAACGGTC-CGGGGCCCGGAACCTTTTCAACTAACGCTATTATTGATACAGTT----TCTGTACTATATTGGTACG
	AF050521.1_T_cruzi_M5631                                     TGTACACAGGCCCCGGTACCCGCGAACAACCCCTCATAAAAATGCGATTTTTGTACACAGGCCCGGGAACCGCGAACAACCCCTCATCAAATTTGAAAACGGTC-CGGGGCCCGGAACTTTTTCAACTAACGCTATTATTGATACAGTT----TCTGTACTATATTGGTACG
	JX154672.1_T_cruzi_Dn_44                                     TGTACACAGGCCCCGGTACCCGCGAACAACCCCTCATAAAAATGCGATTTTTGTACACAGGCCCGGGAACCGCGAACAACCCCTCATCAAATTTGAAAACGGTC-CGGGGCCCGGAACCTTTTCAACTAACGCTATTATTGATACAGTT----TCTGTACTATATTGGTACG
	JX154669.1_T_cruzi_Dn_27                                     TGTACACAGGCCCCGGTACCCGCGAACAACCCCTCATAAAAATGCGATTTTTGTACACAGGCCCGGGAACCGCGAACAACCCCTCATCAAATTTGAAAACGGTC-CGGGGCCCGGAACCTTTTCAACTAACGCTATTATTGATACAGTT----TCTGTACTATATTGGTACG
	RA014_Ja_IL_MF189017                                         -----CGCGGCACCCGGGCCCGCGTACAACCCCTCATAAAAATGGGATTTTTGTACACGGGCCCGGGTGCCGCGAAAAACCCCTCATCAAA-TTGAAAGCGGTT-GTGGCACAAAACCACTTTCAACTAACGCTATTATTGATACAGT----TTCTGTACTATATTGGTAA-
	RA10_Wi_IL_MF189018                                          -------------------CCGCG?ACAACCCCT?ATAAAAATGGGATTTTTGTACACGGGCCCGGGTGCCGCGAAAAACCCCTCATCAAA-TTGAAAGCGGTT-GTGGCACAAAACCACTTTCAACTAACGCTATTATTGATACAGT----TTCTGTACTATATTGGTAA-
	RA4_Ja_IL_MF189019                                           -------------------CCGCG?ACAACCCCT?ATAAAAATGGGATTTTTGTACACGGGCCCGGGTGCCGCGAAAAACCCCTCATCAAA-TTGAAAGCGGTT-GTGGCACAAAACCACTTTCAACTAACGCTATTATTGATACAGT----TTCTGTACTATATTGGTAA-
	RB_KY_MF189020                                               -------------------CCGCG?ACAACCCcT?ATAAAAATGGGATTTTTGtaCaCGGGCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGTT-GTGGCACAAAACCACTTTCAACTAACGCTATTATTGATACAGT----TTCT?TACTATATTGGTAA-
	RA019_MO_MF189021                                            -----CGCGGCACCCGGGCCCGCGTACAACCCCTAATAAAAATGGGATTTTTGTACACGGGCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGTT-GTGGCACAAAACCACTTTCAACTAACGCTATTATTGATACAGT----TTCTGTACTATATTGGTAA-
	RA016_Ja_IL_MF189022                                         ------CGCGCACCCCGGCCCGCGTACAACCCCTAATAAAAATGGGATTTTTGTACACGGGCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGTT-GTGGCACAAAACCACTTTCAACTAACGCTATTATTGATACAGT----TTCTGTACTATATTGGTAA-
	RW_KY_MF189023                                               -------------------CCGCG?ACAACCCCT?ATAAAAATGGGATTTTTGTACACGGGCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGTT-GTGGCACAAAACCACTTTCAACTAACGCTATTATTGATACAGT----TTCT?TACTATATTGGTAA-
	RA15_Ja_IL_MF189024                                          -------------------CCGCG?ACAACCCCT?ATAAAAATGGGATTTTTGTACACGGGCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGTT-GTGGCACAAAACCACTTTCAACTAACCCTATTATTGATACAGT----TTCTGTACTATATTGGTAA-
	Tcruzi_6949_Trypanosoma_cruzi_strain_CL_Brener               TGTACACAGGCCCCAGTGACCGCGTACAACCCCTAATAAAAATGGGGTTTTCGTACACGGTCCCAAGTGCCGCGAAAAACCCCTCATCAAAATTGAAGGCCGTT-GTGGAACACAACCCCTTTCAACTAGCGCTATTATTGATACAGT----TTCTTTACTATATTGGTACG
	AF506368.1_T_cruzi_SL1                                       TGTACACAGGCCCCAGTGACCGCGTACAACCCCTAATAAAAATGGGGTTTTTGTACACGGTCCCAAGTGCCGCAAAAAACCCCTCATCAAAATTGAAAGCCGTT-GTGGGACACAACTCCTTTCAACTAACGCTATTATTGATACAGT----TTCTGTACTATATTGGTACG
	AF051309.1_T_cruzi_MT4183                                    TTTTGTACACAGCCCCGTGCCGCGTACAACCCCTAAT-AAAAATGGGTTTTTGTACACGGTCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGGT-GTGGCGCAACACCGCTTTCAACTAACGCTATTATTGATACAGT----TTCTGTACTATATTGGTACG
	AF051308.1_T_cruzi_MT4181                                    TTGTACACAGCCCCGTGTGCCGCGTACAACCCCTAATAAAAATGGGGTTTTTGTACACGGTCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGGTGGTGGCGCAACACCACTTTCAACTAACGCTATTATTGATACAGT----CTGTACTATAT--TGGTACG
	AF050523.1_T_cruzi_MT4167                                    TTGTACACAGCCCCGGTGGCCGCGTACAACCCCTAATAAAAATGGGGTTTTTGTACACGGTCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGGT-GTGGCGCAACACCACTTTCAACTAACGCTATTATTGATACAGT----TTCTGTACTATATTGGTACG
	AY367124.1_T_cruzi_92122102r                                 TGTACACAGGCCCCGGTGACCGCGTACAACCCCTAATAAAAATGGGATTTTTGTACACGGGCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGTT-GTGGCACAAAACCACTTTC------------------------------------------------
	AY367123.1_T_cruzi_CANIII                                    TGCACACAGGCCCCGGTGGCCGCGTACAACCCCTAATAAAAATGGGGTTTTTGTACACGGTCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGGT-GTGGCACAACACCTCTTTC------------------------------------------------
	KC589110.1_T_cruzi_453                                       TGTACACAGGCCCCGGTGGCCGCGTACAACCCCTAATAAAAATGGGGTTTTTGTACACGGTCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGGT-GTGGCACAACACCACTTTCAACT--------------------------------------------
	KC589112.1_T_cruzi_456                                       TGTACACAGGCCCCGGTGGCCGCGTACAACCCCTAATAAAAATGGGGTTTTTGTACACGGTCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGGT-GTGGCACAACACCACTTTCAAC---------------------------------------------
	KC589111.1_T_cruzi_454                                       TGTACACAGGCCCCGGTGGCCGCGTACAACCCCTAATAAAAATGGGGTTTTTGTACACGGTCCCGGGTGCCGCGAAAAACCCCTCATCAAATTTGAAAGCGGGT-GTGGCACAACACCACTTTCAACTAACGCTATTATTGATACAGT----TTCTGTACTATATTGGTACG

;


END;

begin mrbayes;
	set autoclose=yes nowarn=yes;
	exclude 1-19 149-172; 	
	lset nst=1 rates=equal;
	unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all); 
	prset applyto=(all) ratepr=variable;
	mcmcp ngen= 10000000 relburnin=yes burninfrac=0.25 printfreq=10000  samplefreq=1000 nchains=4 savebrlens=yes;
	mcmc;
	sumt;
end;

[
[[!Likelihood settings from best-fit model (JC) selected by AICcwith jModeltest 0.1.1 on Fri May 12 09:31:58 CDT 2017]

BEGIN PAUP;
Lset base=equal nst=1 rates=equal pinvar=0;
END;]

begin paup;
log start replace=yes file=Tcruzi_18Vdist563.txt; 
  dset dist=abs;
  delete all;
  restore AY367124.1_T_cruzi_92122102r RA014_468 RA10 RA4 RB RA019_ RA016 RW RA15 Tcruzi_6949_Trypanosoma_cruzi_strain_CL_Brener AY367123.1_T_cruzi_CANIII AF050521.1_T_cruzi_M5631;
  exclude missambig;  
  showdist;
log stop;

log start replace=yes file=Tcruzi_18VdistJCA563.txt; 
  dset dist=JC;
  exclude missambig;  
  showdist;
log stop;

log start replace=yes file=Tcruzi_18VdistPA563.txt; 
  dset dist=P;
  exclude missambig;  
  showdist;
log stop;
end;

[[!Likelihood settings from best-fit model (JC) selected by AICcwith jModeltest 0.1.1 on Fri May 12 09:31:58 CDT 2017]
BEGIN PAUP;
Lset base=equal nst=1 rates=equal pinvar=0;
END;]

begin paup;
log start replace=yes file=Tcruzi_18Vdist563.txt; 
  dset dist=abs;
  delete all;
  restore AY367124.1_T_cruzi_92122102r RA014_Ja_IL_MF189017 RA10_Wi_IL_MF189018 RA4_Ja_IL_MF189019 RB_KY_MF189020 RA016_Ja_IL_MF189022 RA019_MO_MF189021 RW_KY_MF189023 RA15_Ja_IL_MF189024 Tcruzi_6949_Trypanosoma_cruzi_strain_CL_Brener AY367123.1_T_cruzi_CANIII AF050521.1_T_cruzi_M5631;
  exclude missambig;  
  showdist;
log stop;

log start replace=yes file=Tcruzi_18VdistJCA563.txt; 
  dset dist=JC;
  exclude missambig;  
  showdist;
log stop;

log start replace=yes file=Tcruzi_18VdistPA563.txt; 
  dset dist=P;
  exclude missambig;  
  showdist;
log stop;
end;


[!Likelihood settings from best-fit model (JC) selected by AICcwith jModeltest 0.1.1 on Fri May 12 09:31:58 CDT 2017]
BEGIN PAUP;
Lset base=equal nst=1 rates=equal pinvar=0;
END;
	exclude 1 - 19 172;	
	delete AY367124.1_T_cruzi_92122102r AY367123.1_T_cruzi_CANIII KC589110.1_T_cruzi_453 KC589112.1_T_cruzi_456;  

log start replace=yes file=Tcruzi_MPlog.txt; 
	set autoclose=yes;
	outgroup AF050522.1_T_cruzi_M6241;
	hsearch addseq=random nreps=1000 swap=tbr hold=1;

   	savetrees file=Tcruzi_MP.tre format=altnex brlens=yes;

    	log stop;

log start replace=yes file=Tcruzi_MPbootstraplog.txt; 
	set autoclose=yes criterion=parsimony root=outgroup storebrlens=yes increase=auto;
	bootstrap nreps=1000 search=heuristic/ addseq=random nreps=10 swap=tbr hold=1;

	savetrees from=1 to=1 file=Tcruzi_MPBootTree.tre format=altnex brlens=yes savebootp=NodeLabels MaxDecimals=0;

    log stop;
    
end;

  log start file=Tcruzi_ML_log.txt;

   set criterion=distance autoclose=yes storebrlens=yes increase=auto root=outgroup;
	exclude 1 - 19 172;	
	delete AY367124.1_T_cruzi_92122102r AY367123.1_T_cruzi_CANIII KC589110.1_T_cruzi_453 KC589112.1_T_cruzi_456;  

   [Set distance=JC objective=ME base=equal rates=equal pinv=0 subst=all negbrlen=setzero;]

   NJ showtree=no breakties=random;

   set criterion=like;

Lset base=equal nst=1 rates=equal pinvar=0;

  hsearch addseq=random nreps=5 swap=tbr;

   savetrees file=Tcruzi_ML_tree.tre format=altnex brlens=yes maxdecimals=6;

 log stop;
	

   log start file=Tcruzi_MLboot_log.txt;

    set criterion=like autoclose=yes storebrlens=yes increase=auto root=outgroup;

    outgroup AF050522.1_T_cruzi_M6241;

	exclude 1 - 19 172;	
	delete AY367124.1_T_cruzi_92122102r AY367123.1_T_cruzi_CANIII KC589110.1_T_cruzi_453 KC589112.1_T_cruzi_456;  

  Lset base=equal nst=1 rates=equal pinvar=0;
  
    bootstrap nreps=1000 search=heuristic/ addseq=random swap=tbr hold=1;

    savetrees from=1 to=1 file=Tcruzi_MLboot_tree.tre format=altnex brlens=yes savebootp=NodeLabels MaxDecimals=0;

    log stop;
    
    END;
    ]