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

From: Gene finding in metatranscriptomic sequences

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
complete=1 train =complete