Table 1.

Key Parameters Controlling HIV-TRACE.

Parameter	Meaning	Phase
−r, --reference	Reference sequence for mapping	Alignment
−m, --minoverlap	Sequences must have at least this many aligned characters	Distance estimation
−a, --ambiguities	Sets policy for handling ambiguous nucleotides	Distance estimation
−g, --fraction	Sets the maximum fraction of resolvable ambiguous nucleotides	Distance estimation
−s, --strip_drams	Mask HIV-1 drug resistance associated sites	Distance estimation
−t, --threshold	Distance threshold for drawing a network link	Network construction
−u, --curate	Sets policy for handling potential contaminants	Network construction