3.2.11 Parameter -q

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3.2.11 Parameter -q

Parameter -q

Function Specifies penalty for a nucleotide mismatch

Default -3

Input format Integer

Example To change nucleotide mismatch penalty to -2, use: -q -2

Parameter	-q
Function	Specifies penalty for a nucleotide mismatch
Default	-3
Input format	Integer
Example	To change nucleotide mismatch penalty to -2, use: -q -2

Note:

Different -r/-q ratio is optimal for alignments with different percent of identities. Restrictions on input values for -r/-q as well as -G/-E were introduced in 2.2.13 release. See Table 5.2 for details.

Tao Tao 2006-12-29