3.2.12 Parameter -r

Next: 3.2.13 Parameter -v Up: 3.2 Individual command line Previous: 3.2.11 Parameter -q Contents Index

3.2.12 Parameter -r

Parameter -r

Function Specifies reward for a nucleotide match

Default 1

Input format Integer

Example To increase the nucleotide match reward to 2, use: -r 2

Parameter	-r
Function	Specifies reward for a nucleotide match
Default	1
Input format	Integer
Example	To increase the nucleotide match reward to 2, use: -r 2

Note:

Different -r/-q ratio is optimal for finding alignment with different percent identity, 1/-3 for 99%, 2/-5 for 98%, 1/-2 for 95%, 2/-3 for 90%, 4/-5 for 80-85%, 1/-1 for 75%, and 5/-4 for 65%. Only a limited set of -r/-q is supported.

Tao Tao 2006-12-29