This section is simply a sorted and extended version of the scanps_alias.dat file. New commands may from time to time get added to that file, so look there if something does not makes sense.
APPLY_INDEX apply_index Flag when creating database in mode 99 if =1 then the characters used to represent the amino acids in the binary sequence database are converted to allow fast indexing of the pairscore matrix. This is the default. If you use a lot of different pairscore matrices with different index strings, then set this to zero. APRINT_TO_THRESHOLD aprint_to_threshold aptt Flag to specify if alignments will be printed down to the probability threshold defined by PROBCUT. AUTO_CORNER auto_corner # Obsolete BDB_ROOT bdb_root bdb Name of root name for binary database files - e.g. sprot would mean there is a file called sprot.bix and sprot.bsq. BLOCK_FILE_OUT block_file_out bfo Name for a file to contain multiple alignment output in AMPS block file format. CALEB_LPLBUCKETWIDTH buckwidth # logprodlen bucket width CALEB_MINBUCK minbuck # minimum number needed for a stats bucket. CALEB_MINRANGE minrange # minimum number of buckets needed for fitting. CALEB_PRINT caleb_print # print out the caleb stats files. 1 = yes, 0 = no. Options related to the Webber and Barton on-the-fly statistics. CODON_FILE codon_file #Translation table for DNA to Protein COMPLEMENT_QUERY comp_query cq # scan with complement of DNA query CUT_CONSTANT cut_constant # Obsolete CUT_CORNERS cut_corners # Obsolete DB_DIR db_dir Directory for storing database files. DB_FILE db_file d Sequence database filename - name for file that is not a binary database file. DB_FORMAT DB_F db_format dbf As for QSEQ_FORMAT - the format of the database sequence. DO_SORT do_sort # Obsolete. DO_STATS do_stats This should always be set to 2. DUMP_STATS dump_stats # Obsolete. EPB_PEN epb_pen # Obsolete. EPL_PEN epl_pen # Obsolete. EPR_PEN epr_pen # Obsolete. EPT_PEN ept_pen # Obsolete. EXTRACT_FILE extract_file efile # Obsolete. EXTRACT_SEQ extract_seq eseq # Obsolete. EXTRACT_SEQ_FORMAT extract_seq_format # Obsolete. FAST fast # Obsolete. FIND_REPEATS find_repeats # Obsolete. FIT_FILE fit_file # Obsolete. FIT_TYPE fit_type # Obsolete. FRAG_FILE_FORMAT frag_file_format fff Format of the frag file optionally output for a profile alignment 0 for PIR 1 for FASTA. FRAG_FILE_OUT frag_file_out ffo # the name of the frag file to output FSE_PEN fse_pen # Obsolete. FS_PEN fs_pen FSC_PEN fsc_pen Penalty for frame shift creation in DNA vs Protein modes. GAP_CHARACTER GAP_CHAR gap_character gap_char Character used to show a gap. GENERAL_DIR gen_dir Directory to store miscellaneous information in - e.g. the codon.dat file. LD_PEN ld_pen e_pen E_PEN Length dependent (extension) gap penalty LICENSE_DIR license_dir # Obsolete. LI_PEN li_pen c_pen C_PEN Length independent (creation) gap penalty LOG_SCORES log_scores lns # Obsolete. MATRIX_DIR matrix_dir md Directory that contains pairscore matrices. MATRIX_FILE matrix_file m Name of pairscore matrix file. MATRIX_FORMAT matrix_format mf Format of matrix file =0 for PIR =1 for NCBI/BLAST MAX_AOUT max_aout maout Max number of alignments to output - works in conjunction with -aptt option. MAX_BLOC_SEQ max_bloc_seq max_blc_seq # Not used. MAX_ID_LEN max_id_len Maximum length for sequence identifiers MAX_NOUT max_nout mnout Max number of sequences to output in score list (works with -nptt). MAX_NSEQ max_nseq Maximum number of sequences allowed in program - this must be bigger than the database size. MAX_SEQ_LEN max_seq_len Max allowed length for an amino acid sequence. In most compiled programs this has a precompiled limit. If the program is compiled without MMX/SSE support or parallel processing support, then this variable can be set. MAX_TITLE_LEN max_title_len #Maximum length for sequence titles MIN_ASCORE min_ascore # Obsolete. MIN_LEN min_len # Minimum length allowed for an alignment MIN_NSTATS min_nstats # Obsolete. MIN_SCORE min_score # Minimum score required for score list to be output MIXED_MODE mixed_mode mm # When set to 1 and mode 202 is active, first iteration is mode 202 others are mode 200. MM_LD_PEN mm_ld_pen mmpen Length dependent penalty to use in MIXED_MODE on iterations 1-N MODE mode Specify type of scan or processing - see manual above. MULTIPLE_OUTPUT_LENGTH multiple_output_length mol Output length for multiple alignments NCHUNK nchunk MPI chunk size - number of sequences to send to each processor in each parallel chunk. NITER niter Number of iterations to do. NPRINT_TO_THRESHOLD nprint_to_threshold nptt If 1 then output is down to probcut threshold if 0 then MAX_NOUT is used NRANS nrans # Obsolete. OSEQ_FILE oseq_file # Obsolete. OUTPUT_LENGTH output_length out_len OUT_LEN Output length for pairwise alignments. PCUT pcut # Obsolete. PEN_FACTOR pen_factor penf Factor to modify observed gap penalties in modes 210/212 PIDTHRESH pidthresh pidt percentage identity threshold for inclusion in profile. POSWGTFAC poswgtfac pwf # profile position specific weighting factor PRECISION precision precis PRECIS Precision - all floats multiplied by this number. Usually 100. PRED_FILE pred_file # Obsolete. PRINT_ALIGN print_align # Obsolete. PRINT_BLOCK_FILE print_block_file pbf If 1 then will print an AMPS block file for the multiple alignment. PRINT_FRAG_FILE print_frag_file pff If 1 then will print a file of seq fragments in format. See manual. PRINT_FRQ_TABS print_frq_tabs Print out the frequency tables in an iterated search. PRINT_PROFILES print_profiles Print out the lookup tables in iterated search. PROBCUT probcut eval Probability or eval cutoff for do_stats 1 or 2. PROBCUT2 probcut2 eval2 Probability or eval cutoff for inclusion in profile. PROB_TYPE prob_type prob type 0=probs 1 =oldevals 2 =newevals - only prob_type 2 is tested. PROFILE_WEIGHT_METHOD profile_weight_method pwm 0 for original weighting 1 for HH. QBLC_FILE qblc_file QBLC # Obsolete. QBLC_FORMAT QBLC_F qblc_format # Obsolete. QSEQ_FILE qseq_file QSEQ qseq s S Query sequence file. QSEQ_FORMAT QSEQ_F qseq_format qsf 0 = PIR format, 1 = FASTA format READ_PRED read_pred # Obsolete. ROBSIM robsim # Obsolete. RUN_SW_MIN run_sw_min # Threshold required before NALL algorithm runs SAVE_PROFILES save_profiles # Obsolete. SCAN scan # Obsolete. SEC_FILE sec_file # Obsolete. SHOW_BLURB show_blurb If set to 0 then no info is printed to output file. SHOW_IDENT_WIDTH show_ident_width siw The width of the ident string to output. SHOW_LEN show_len lens # Obsolete. SHOW_PMATRIX show_pmatrix spm Print pairscore matrix to output file (requires SHOW_BLURB). SHOW_TITLES show_titles titles Print titles in output. SHOW_TITLES_WIDTH show_titles_width stw The width of the title string to output. SPECIAL special # Obsolete. STDERR stderr # redefinition of stderr STDIN stdin # redefinition of stdin STDOUT stdout # redefinition of stdout STOP_WEIGHT stop_weight sw # Weight for matching amino acid to STOP codon (MODE 22). TEST #Test - no alias TIME time # Set to 1 to record CPU times TOP_CUTFRAC top_cutfrac # Obsolete. TOP_ONLY top_only 1 for only top scoring alignment in each pair. 0 for all alignments down to probcut. USE_GAPDEFS use_gapdefs ugd if = 1 then use scanps_Gapdefs.dat values if posssible VERBOSE verbose If >=1 then print various messages as program runs. VINGRON_FILE vingron_file # Obsolete.