Sample: BlastFile with 1 to 10.000 result items

Mode	1	10	100	1000	10000
flex	0.003	0.015	0.199	1.979	25.548
flex-tcl	0.005	0.018	0.167	1.775	20.701
gcj	0.099	0.149	0.784	7.536	83.421
gij	0.109	0.482	4.917	51.939	nd
java	0.228	0.348	0.753	3.048	27.806
javaip	0.180	0.517	4.715	49.852	nd
plex	0.011	0.082	0.856	9.565	107.987
perl	0.031	0.050	0.235	2.280	23.916
re2c	0.004	0.012	0.076	0.765	8.438
tcl	1.702	12.524	140.249	nd	nd

The Re2c based scanner is the fastest, but the setup and the coding is more complicated than for the other scanners.
Flex-based scanners are 2-3 times slower than Re2c based scanners, regardless if there is an embedded Tcl-interpreter for better string handling (flex-tcl), Jflex code (java), executed with the Sun-Java Hotspot virtual machine (1.5) as well as to machine code compiled Jflex code (java-gcj) and Plex (sbs-plex = Pascal lex) based scanners are about 5 and 10 times slower than Re2c based scanners. Interpreted Java-Code either executed with the Sun-interpreter (java-ip = “java -Xint”) or with the gnu-interpreter (java-gij) is about 50 times slower than Re2c-Code. The Tcl based scanner is about 1000 times slower than the Re2c based. The per scanner is a line based scanner thereof not able to do complicated scanning with more than two states or patterns on the same line.