#NEXUS

BEGIN TAXA;
	TITLE Taxa;
	DIMENSIONS NTAX=17;
	TAXLABELS
		Cotton_leafroll_dwarf_virus_ARG Cotton_leafroll_dwarf_virus_CV2 Cotton_leafroll_dwarf_virus_PL3 Cotton_leafroll_dwarf_virus_PL5 Cotton_leafroll_dwarf_virus_PL6 Cotton_leafroll_dwarf_virus_PL7 Cotton_leafroll_dwarf_virus_PL8 Cotton_leafroll_dwarf_virus_PL9 Cotton_leafroll_dwarf_virus_PO1 Cotton_leafroll_dwarf_virus_PV1 Cotton_leafroll_dwarf_virus_Ron1 Cotton_leafroll_dwarf_virus_Ron10 Cotton_leafroll_dwarf_virus_Ron11 Cotton_leafroll_dwarf_virus_Ron12 Cotton_leafroll_dwarf_virus_Ron3 Cotton_leafroll_dwarf_virus_Ron4 Cotton_leafroll_dwarf_virus_Ron9 
	;
END;

BEGIN CHARACTERS;
	TITLE  MP_Matrix;
	DIMENSIONS  NCHAR=174;
	FORMAT DATATYPE = Protein GAP = - MISSING = ?;
	MATRIX
	Cotton_leafroll_dwarf_virus_ARG    MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMEYSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLTNSESPRMGGSNLRRLSSMDRNGMTPPRTNSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_CV2    MEEDDHVDATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELRARHLFSQKTISREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCLPSPPLLINSESPRTGGSNLRRLLSTDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_PL3    MEEDDHVDATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELRARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLTNSESPRMGGNSLQRLSLTDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_PL5    MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPFPPRLTNSESPRMGGNNLRRLSSMDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_PL6    MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPFPPRLTNSESPRMGGNNLRRLSSMDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_PL7    MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPLRLTNSESPRMGGSNLRRLSSMDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_PL8    MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLTNSESPRMGGSNLRRLSSMDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_PL9    MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPFPPRLTNSESPRMGGNNLRRLSSMDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_PO1    MEEDDHVDATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELRARHLFSQKTISREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCLPSPPLLINSESPRTGGSNLRRLSSTDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_PV1    MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLTNSESPRTGGSNLRRLSSMDRNGMTPPRTSSESYIKAMVPRR
	Cotton_leafroll_dwarf_virus_Ron1   MEEDDHVGATGVGKISQWLWSKPLGTHNAEEDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPFPPRLTNSESPRMGGSNLRRLSSMDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_Ron10  MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLINSESPRMGGSNLRRLSSTDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_Ron11  MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSVMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLTNSESPRMGGSNLRRLSSTDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_Ron12  MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLTNSESPRMGGSNLRRLSSMDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_Ron3   MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLTNSESPRMGGSNLRRLSSTDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_Ron4   MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLTNSESPRMGGSNLRRLSSTDRNGMTPPRTSSESYTKAMVPRR
	Cotton_leafroll_dwarf_virus_Ron9   MEEDDHVGATGVGKISQWLWSKPLGTHNAEDDEDEEVVIGQEDAFLEDQELQARHLFSQKTVSREVPQDQSRSGRLYQIARHSAMECSRPTMNIRSQWSYWSSSPRPLQHPPVPSLTKWIHTVNCQPYPPRLTNSESPRMGGSNLRRLSSMDRNGMTPPRTSSESYTKAMVPRR
;
END;

BEGIN TREES;
	Title NJ_Result;
	LINK Taxa = Taxa;
	TRANSLATE
		1 Cotton_leafroll_dwarf_virus_ARG,
		2 Cotton_leafroll_dwarf_virus_CV2,
		3 Cotton_leafroll_dwarf_virus_PL3,
		4 Cotton_leafroll_dwarf_virus_PL5,
		5 Cotton_leafroll_dwarf_virus_PL6,
		6 Cotton_leafroll_dwarf_virus_PL7,
		7 Cotton_leafroll_dwarf_virus_PL8,
		8 Cotton_leafroll_dwarf_virus_PL9,
		9 Cotton_leafroll_dwarf_virus_PO1,
		10 Cotton_leafroll_dwarf_virus_PV1,
		11 Cotton_leafroll_dwarf_virus_Ron1,
		12 Cotton_leafroll_dwarf_virus_Ron10,
		13 Cotton_leafroll_dwarf_virus_Ron11,
		14 Cotton_leafroll_dwarf_virus_Ron12,
		15 Cotton_leafroll_dwarf_virus_Ron3,
		16 Cotton_leafroll_dwarf_virus_Ron4,
		17 Cotton_leafroll_dwarf_virus_Ron9;
	TREE PAUP_1 = ((2:0.00575586,9:1.0E-8):0.014654785,(3:0.0292066,(12:9.8E-7,((13:0.00575786,(15:1.0E-8,16:1.0E-8):1.0E-8):1.0E-8,(10:0.01155874,((11:0.00577346,(8:1.0E-8,(4:1.0E-8,5:1.0E-8):1.0E-8):0.0057557):0.00579248,(1:0.01154425,(7:1.0E-8,(6:0.00576908,(14:1.0E-8,17:1.0E-8):1.0E-8):1.0E-8):1.0E-8):1.0E-8):1.0E-8):0.00575997):0.00575612):0.01154085):0.014654785)[% ] [% ] [%  setBetweenBits = selected ];
END;