glimmer

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USAGE:  glimmer3 [options] <sequence-file> <icm-file> <tag>

Read DNA sequences in <sequence-file> and predict genes
in them using the Interpolated Context Model in <icm-file>.
Output details go to file <tag>.detail and predictions go to
file <tag>.predict

Options:
-A <codon-list>
--start_codons <codon-list>
   Use comma-separated list of codons as start codons
   Sample format:  -A atg,gtg
   Use -P option to specify relative proportions of use.
   If -P not used, then proportions will be equal
-b <filename>
--rbs_pwm <filename>
   Read a position weight matrix (PWM) from <filename> to identify
   the ribosome binding site to help choose start sites
-C <p>
--gc_percent <p>
   Use <p> as GC percentage of independent model
   Note:  <p> should be a percentage, e.g., -C 45.2
-E <filename>
--entropy <filename>
   Read entropy profiles from <filename>.  Format is one header
   line, then 20 lines of 3 columns each.  Columns are amino acid,
   positive entropy, negative entropy.  Rows must be in order
   by amino acid code letter
-f
--first_codon
   Use first codon in orf as start codon
-g <n>
--gene_len <n>
   Set minimum gene length to <n>
-h
--help
   Print this message
-i <filename>
--ignore <filename>
   <filename> specifies regions of bases that are off
   limits, so that no bases within that area will be examined
-l
--linear
   Assume linear rather than circular genome, i.e., no wraparound
-L <filename>
--orf_coords <filename>
   Use <filename> to specify a list of orfs that should
   be scored separately, with no overlap rules
-M
--separate_genes
   <sequence-file> is a multifasta file of separate genes to
   be scored separately, with no overlap rules
-o <n>
--max_olap <n>
   Set maximum overlap length to <n>.  Overlaps this short or shorter
   are ignored.
-P <number-list>
--start_probs <number-list>
   Specify probability of different start codons (same number & order
   as in -A option).  If no -A option, then 3 values for atg, gtg and ttg
   in that order.  Sample format:  -P 0.6,0.35,0.05
   If -A is specified without -P, then starts are equally likely.
-q <n>
--ignore_score_len <n>
   Do not use the initial score filter on any gene <n> or more
   base long
-r
--no_indep
   Don't use independent probability score column
-t <n>
--threshold <n>
   Set threshold score for calling as gene to n.  If the in-frame
   score >= <n>, then the region is given a number and considered
   a potential gene.
-X
--extend
   Allow orfs extending off ends of sequence to be scored
-z <n>
--trans_table <n>
   Use Genbank translation table number <n> for stop codons
-Z <codon-list>
--stop_codons <codon-list>
   Use comma-separated list of codons as stop codons
   Sample format:  -Z tag,tga,taa