maker_opts.ctl

#-----Genome (these are always required)
genome=pg29-plastid.fa #genome sequence (fasta file or fasta embeded in GFF3 file)
organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic

#-----EST Evidence (for best results provide a file for at least one)
est=NC_021456.frn #set of ESTs or assembled mRNA-seq in fasta format

#-----Protein Homology Evidence (for best results provide a file for at least one)
protein=cds_aa.fa #protein sequence file in fasta format (i.e. from mutiple oransisms)

#-----Repeat Masking (leave values blank to skip repeat masking)
model_org=
repeat_protein=

#-----Gene Prediction
est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=1 #infer predictions from protein homology, 1 = yes, 0 = no

#-----MAKER Behavior Options
est_forward=1 #map names and attributes forward from EST evidence, 1 = yes, 0 = no
single_exon=1 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no
single_length=50 #min length required for single exon ESTs if 'single_exon is enabled'