GLAM2: Find gapped local alignment motifs Options: -alpha [DNA|PROTEIN] Alphabet; default DNA -min_seqs Minimum number of sequences in an alignment (-z) -min_cols Minimum number of aligned columns (-a) -max_cols Maximum number of aligned columns (-b) -initial_cols Initial number of aligned columns (-w) -runs Number of alignment replicates (-r) -run_no_impr Number of iterations without improvement (-n) -del_pseudo Deletion pseudocount (-D) -no_del_pseudo No-deletion pseudocount (-E) -ins_pseudo Insertion pseudocount (-I) -no_ins_pseudo No-insertion pseudocount (-J) -rev_comp Check both strands (-2) -embed Embed the sequences (-M) -help brief help message ]]> rev_comp -rev_comp false Check both strands embed -embed true Embed the sequences in the HTML output alpha -alpha STRING DNA PROTEIN DNA Alphabet min_seqs -min_seqs INT Minimum sequences in an alignment min_cols -min_cols INT Minimum number of aligned columns max_cols -max_cols INT Maximum number of aligned columns initial_cols -initial_cols INT Initial number of aligned columns runs -runs INT Number of alignment replicates run_no_impr -run_no_impr INT Number of iterations without improvement del_pseudo -del_pseudo FLOAT Deletion pseudocount no_del_pseudo -no_del_pseudo FLOAT No-deletion pseudocount ins_pseudo -ins_pseudo FLOAT Insertion pseudocount no_ins_pseudo -no_ins_pseudo FLOAT No-insertion pseudocount sequences FILE INPUT Input sequences g1 sequences alpha rev_comp embed Sequences g2 min_seqs min_cols max_cols initial_cols Alignment Constraints g4 del_pseudo no_del_pseudo ins_pseudo no_ins_pseudo Alignment Pseudocounts g3 runs run_no_impr Alignment Attempts @SERVICE_DIR@/glam2_webservice false