IMGC_XSEDE


infile.fas -s (default) -i 1 (default) -o 3 -p 6 -f (default)				
	
<!--            (-w) [weeds out individuals; maintains original sequence length (fast)]
                (-s) [weeds out both individuals and sites; makes the largest block possible; (slow)]
                (-i 1.1 [weights keeping individuals. Default = 1. Weights keeping individuals vs keeping sites]
                (-o 0 [omits the nth id from your fasta file when optimizing the region, but tacks them back on in the output]
                (-p 0 [preserves the pth id from your fasta file no matter what]
                (-f) [prints output in fasta format (not IM)] -->
                
maintain_seqlength_ - (switch) Weed out individuals; maintains original sequence length (fast; -w)default=0
weed_individandsites_ - (switch)
Weed out both individuals and sites; make the largest block possible; (slow, -s) default=1
(You can't choose both -w and -s options)
		
weight_keepindivid_ - float Weight keeping individuals -i $value (default=1)
		
<!-- (-o 0 [omits the nth id from your fasta file when optimizing the region, but tacks them back on in the output] -->
omit_nthid_ - Integer Omit the nth id from the fasta file when optimizing -o $value

<!-- (-p 0 [preserves the pth id from your fasta file no matter what] -->
preserve_pthid_ - Integer - Preserve the pth id "-p $value
		
<!--  (-f) [prints output in fasta format (not IM)] -->
print_fatsaformat_ - Switch; Print the output in fasta format (-f)