--- /dev/null
+ /local/gjb_lab/blast+/bin/psiblast -help\r
+USAGE\r
+ psiblast [-h] [-help] [-import_search_strategy filename]\r
+ [-export_search_strategy filename] [-db database_name]\r
+ [-dbsize num_letters] [-gilist filename] [-negative_gilist filename]\r
+ [-entrez_query entrez_query] [-subject subject_input_file]\r
+ [-subject_loc range] [-query input_file] [-out output_file]\r
+ [-evalue evalue] [-word_size int_value] [-gapopen open_penalty]\r
+ [-gapextend extend_penalty] [-xdrop_ungap float_value]\r
+ [-xdrop_gap float_value] [-xdrop_gap_final float_value]\r
+ [-searchsp int_value] [-seg SEG_options] [-soft_masking soft_masking]\r
+ [-matrix matrix_name] [-threshold float_value] [-culling_limit int_value]\r
+ [-best_hit_overhang float_value] [-best_hit_score_edge float_value]\r
+ [-window_size int_value] [-lcase_masking] [-query_loc range]\r
+ [-parse_deflines] [-outfmt format] [-show_gis]\r
+ [-num_descriptions int_value] [-num_alignments int_value] [-html]\r
+ [-max_target_seqs num_sequences] [-num_threads int_value] [-remote]\r
+ [-comp_based_stats compo] [-use_sw_tback] [-gap_trigger float_value]\r
+ [-num_iterations int_value] [-out_pssm checkpoint_file]\r
+ [-out_ascii_pssm ascii_mtx_file] [-in_msa align_restart]\r
+ [-in_pssm psi_chkpt_file] [-pseudocount pseudocount]\r
+ [-inclusion_ethresh ethresh] [-phi_pattern file] [-version]\r
+\r
+DESCRIPTION\r
+ Position-Specific Initiated BLAST 2.2.22+\r
+\r
+OPTIONAL ARGUMENTS\r
+ -h\r
+ Print USAGE and DESCRIPTION; ignore other arguments\r
+ -help\r
+ Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments\r
+ -version\r
+ Print version number; ignore other arguments\r
+\r
+ *** Input query options\r
+ -query <File_In>\r
+ Input file name\r
+ Default = `-'\r
+ * Incompatible with: in_msa, in_pssm\r
+ -query_loc <String>\r
+ Location on the query sequence (Format: start-stop)\r
+\r
+ *** General search options\r
+ -db <String>\r
+ BLAST database name\r
+ * Incompatible with: subject, subject_loc\r
+ -out <File_Out>\r
+ Output file name\r
+ Default = `-'\r
+ -evalue <Real>\r
+ Expectation value (E) threshold for saving hits\r
+ Default = `10'\r
+ -word_size <Integer, >=2>\r
+ Word size for wordfinder algorithm\r
+ -gapopen <Integer>\r
+ Cost to open a gap\r
+ -gapextend <Integer>\r
+ Cost to extend a gap\r
+ -matrix <String>\r
+ Scoring matrix name\r
+ Default = `BLOSUM62'\r
+ -threshold <Real, >=0>\r
+ Minimum word score such that the word is added to the BLAST lookup table\r
+ -comp_based_stats <String>\r
+ Use composition-based statistics for blastp / tblastn:\r
+ D or d: default (equivalent to 2)\r
+ 0 or F or f: no composition-based statistics\r
+ 1: Composition-based statistics as in NAR 29:2994-3005, 2001\r
+ 2 or T or t : Composition-based score adjustment as in Bioinformatics\r
+ 21:902-911,\r
+ 2005, conditioned on sequence properties\r
+ 3: Composition-based score adjustment as in Bioinformatics 21:902-911,\r
+ 2005, unconditionally\r
+ For programs other than tblastn, must either be absent or be D, F or 0\r
+ Default = `2'\r
+\r
+ *** BLAST-2-Sequences options\r
+ -subject <File_In>\r
+ Subject sequence(s) to search\r
+ * Incompatible with: db, gilist, negative_gilist\r
+ -subject_loc <String>\r
+ Location on the subject sequence (Format: start-stop)\r
+ * Incompatible with: db, gilist, negative_gilist, remote\r
+\r
+ *** Formatting options\r
+ -outfmt <String>\r
+ alignment view options:\r
+ 0 = pairwise,\r
+ 1 = query-anchored showing identities,\r
+ 2 = query-anchored no identities,\r
+ 3 = flat query-anchored, show identities,\r
+ 4 = flat query-anchored, no identities,\r
+ 5 = XML Blast output,\r
+ 6 = tabular,\r
+ 7 = tabular with comment lines,\r
+ 8 = Text ASN.1,\r
+ 9 = Binary ASN.1\r
+ 10 = Comma-separated values\r
+\r
+ Options 6, 7, and 10 can be additionally configured to produce\r
+ a custom format specified by space delimited format specifiers.\r
+ The supported format specifiers are:\r
+ qseqid means Query Seq-id\r
+ qgi means Query GI\r
+ qacc means Query accesion\r
+ sseqid means Subject Seq-id\r
+ sallseqid means All subject Seq-id(s), separated by a ';'\r
+ sgi means Subject GI\r
+ sallgi means All subject GIs\r
+ sacc means Subject accession\r
+ sallacc means All subject accessions\r
+ qstart means Start of alignment in query\r
+ qend means End of alignment in query\r
+ sstart means Start of alignment in subject\r
+ send means End of alignment in subject\r
+ qseq means Aligned part of query sequence\r
+ sseq means Aligned part of subject sequence\r
+ evalue means Expect value\r
+ bitscore means Bit score\r
+ score means Raw score\r
+ length means Alignment length\r
+ pident means Percentage of identical matches\r
+ nident means Number of identical matches\r
+ mismatch means Number of mismatches\r
+ positive means Number of positive-scoring matches\r
+ gapopen means Number of gap openings\r
+ gaps means Total number of gaps\r
+ ppos means Percentage of positive-scoring matches\r
+ frames means Query and subject frames separated by a '/'\r
+ qframe means Query frame\r
+ sframe means Subject frame\r
+ When not provided, the default value is:\r
+ 'qseqid sseqid pident length mismatch gapopen qstart qend sstart send\r
+ evalue bitscore', which is equivalent to the keyword 'std'\r
+ Default = `0'\r
+ -show_gis\r
+ Show NCBI GIs in deflines?\r
+ -num_descriptions <Integer, >=0>\r
+ Number of database sequences to show one-line descriptions for\r
+ Default = `500'\r
+ -num_alignments <Integer, >=0>\r
+ Number of database sequences to show alignments for\r
+ Default = `250'\r
+ -html\r
+ Produce HTML output?\r
+\r
+ *** Query filtering options\r
+ -seg <String>\r
+ Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or\r
+ 'no' to disable)\r
+ Default = `no'\r
+ -soft_masking <Boolean>\r
+ Apply filtering locations as soft masks\r
+ Default = `false'\r
+ -lcase_masking\r
+ Use lower case filtering in query and subject sequence(s)?\r
+\r
+ *** Restrict search or results\r
+ -gilist <String>\r
+ Restrict search of database to list of GI's\r
+ * Incompatible with: negative_gilist, remote, subject, subject_loc\r
+ -negative_gilist <String>\r
+ Restrict search of database to everything except the listed GIs\r
+ * Incompatible with: gilist, remote, subject, subject_loc\r
+ -entrez_query <String>\r
+ Restrict search with the given Entrez query\r
+ * Requires: remote\r
+ -culling_limit <Integer, >=0>\r
+ If the query range of a hit is enveloped by that of at least this many\r
+ higher-scoring hits, delete the hit\r
+ * Incompatible with: best_hit_overhang, best_hit_score_edge\r
+ -best_hit_overhang <Real, (>=0 and =<0.5)>\r
+ Best Hit algorithm overhang value (recommended value: 0.1)\r
+ * Incompatible with: culling_limit\r
+ -best_hit_score_edge <Real, (>=0 and =<0.5)>\r
+ Best Hit algorithm score edge value (recommended value: 0.1)\r
+ * Incompatible with: culling_limit\r
+ -max_target_seqs <Integer, >=1>\r
+ Maximum number of aligned sequences to keep\r
+\r
+ *** Statistical options\r
+ -dbsize <Int8>\r
+ Effective length of the database\r
+ -searchsp <Int8, >=0>\r
+ Effective length of the search space\r
+\r
+ *** Search strategy options\r
+ -import_search_strategy <File_In>\r
+ Search strategy to use\r
+ * Incompatible with: export_search_strategy\r
+ -export_search_strategy <File_Out>\r
+ File name to record the search strategy used\r
+ * Incompatible with: import_search_strategy\r
+\r
+ *** Extension options\r
+ -xdrop_ungap <Real>\r
+ X-dropoff value (in bits) for ungapped extensions\r
+ -xdrop_gap <Real>\r
+ X-dropoff value (in bits) for preliminary gapped extensions\r
+ -xdrop_gap_final <Real>\r
+ X-dropoff value (in bits) for final gapped alignment\r
+ -window_size <Integer, >=0>\r
+ Multiple hits window size, use 0 to specify 1-hit algorithm\r
+ -gap_trigger <Real>\r
+ Number of bits to trigger gapping\r
+ Default = `22'\r
+\r
+ *** Miscellaneous options\r
+ -parse_deflines\r
+ Should the query and subject defline(s) be parsed?\r
+ -num_threads <Integer, >=1>\r
+ Number of threads to use in the BLAST search\r
+ Default = `1'\r
+ * Incompatible with: remote\r
+ -remote\r
+ Execute search remotely?\r
+ * Incompatible with: gilist, negative_gilist, subject_loc, num_threads,\r
+ num_iterations\r
+ -use_sw_tback\r
+ Compute locally optimal Smith-Waterman alignments?\r
+\r
+ *** PSI-BLAST options\r
+ -num_iterations <Integer, >=1>\r
+ Number of iterations to perform\r
+ Default = `1'\r
+ * Incompatible with: remote\r
+ -out_pssm <File_Out>\r
+ File name to store checkpoint file\r
+ -out_ascii_pssm <File_Out>\r
+ File name to store ASCII version of PSSM\r
+ -in_msa <File_In>\r
+ File name of multiple sequence alignment to restart PSI-BLAST\r
+ * Incompatible with: in_pssm, query\r
+ -in_pssm <File_In>\r
+ PSI-BLAST checkpoint file\r
+ * Incompatible with: in_msa, query, phi_pattern\r
+\r
+ *** PSSM engine options\r
+ -pseudocount <Integer>\r
+ Pseudo-count value used when constructing PSSM\r
+ Default = `0'\r
+ -inclusion_ethresh <Real>\r
+ E-value inclusion threshold for pairwise alignments\r
+ Default = `0.002'\r
+\r
+ *** PHI-BLAST options\r
+ -phi_pattern <File_In>\r
+ File name containing pattern to search\r
+ * Incompatible with: in_pssm\r
git://source.jalview.org / jabaws.git / blobdiff