Table 1 Command lines and parameters used for the programs in the benchmarking.

GeneMark:

$ gmsn.pl −− prok −− format GFF < input>

Glimmer:

$ build − icm − r run1.icm < < coding− sequences>

$ glimmer3 − o50 − g110 − t30 < input> run1.icm run1

MetaGeneMark:

$ gmhmmp − s . − f G − m MetaGeneMark v1 . mod − o mgm.gff < input>

FragGeneScan:

$ run_FragGeneScan.pl − genome=< input> − out=Frag