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#NEXUS 
Begin data;
	Dimensions ntax=5 nchar=80;
	Format datatype=dna symbols="ACTG" missing=? gap=-;
	Matrix
[YAL053W, 25, ...]
Scer TCTTTATTGACGTGTATGGACAATT
Spar TCTTTGTTAACGTGCATGGACAATT
Smik TCCTTGCTAACATGCATGGACAATT
Skud TCTTTGCTAACGTGCATGGATAATT
Sbay TCTTTACTAACGTGCATGGATAACT
[YAR007C, 30]
Scer ATGAGCAGTGTTCAACTTTCGAGGGGCGAT
Spar ATGAGCAGCGTTCAACTTTCGAAGGGCGAC
Smik ATGAGCAGCGTGCAACTATCAAAGGGCGAC
Skud ATGAGCAGTGTTCAACTTTCGAAGGGCGAC
Sbay ATGAGCAGCGTTCAACTTTCGAAGGGCGAC
[YBL015W, 25]
Scer TCTAATTTGTTAAAGCAGAGAGTTA
Spar TCTAATTTGTTAAAGCAGAGAGTTA
Smik TCTAATTTGTTAAAACAGAGAGTTC
Skud TCTAATCTGTTGAAGCAGAGAGTTA
Sbay TCTAATCTGTTGAAGCAAAAAGTCA
;End;
BEGIN PHYLONET;  
MCMC_SEQ -loci (YBL015W,YAR007C) -cl 550000 -bl 50000 -sf 5000;
END;