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parameters.php
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>locBLAST - Local NCBI BLAST+ Search</title>
<link href="style.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div class="output">
<h2 style="text-align: center;"><i style="font-size: medium">loc</i><span style="color:blue; font-size: large">BLAST</span> - <span style="font-size: large;">local NCBI BLAST</span></h2>
<hr class="heffect" />
<div style="font: 90%/1.5 arial, tahoma, verdana, sans-serif;">
<a href="index.php" title="Go Back to Home"><div style="padding: 0 5px 0 0;" id="back"></div></a>
<h4 style="text-align:center; color:blue" id="top">Advanced BLAST Search Options</h4>
<ol>
<li><a href="#blastn">BlastN - Commandline Parameters</a></li>
<li><a href="#blastp">BlastP - Commandline Parameters</a></li>
<li><a href="#blastx">BlastX - Commandline Parameters</a></li>
<li><a href="#tblastn">tBlastN - Commandline Parameters</a></li>
<li><a href="#tblastx">tBlastX - Commandline Parameters</a></li>
<li><a href="#deltablast">DeltaBlast - Commandline Parameters</a></li>
<li><a href="#psiblast">PSI-Blast - Commandline Parameters</a></li>
<li><a href="#rpsblast">RPS-Blast - Commandline Parameters</a></li>
<li><a href="#rpstblastn">RPS-tBlastn - Commandline Parameters</a></li>
</ol>
<hr style="background-image: linear-gradient(to right, white, blue, white); color: blue; height: 1px; border: 0;"/>
<h4 style="text-align:center; color:blue;" id="blastn">BlastN - Commandline Parameters</h4>
<div style="padding: 0 15px 0 15px;">
blastn [<b>‑h</b>] [<b>‑help</b>]<br/>
[<b>‑import_search_strategy</b> filename]<br/>
[<b>‑export_search_strategy</b> filename]<br/>
[<b>‑task</b> task_name]<br/>
[<b>‑db</b> database_name]<br/>
[<b>‑dbsize</b> num_letters]<br/>
[<b>‑gilist</b> filename]<br/>
[<b>‑seqidlist</b> filename]<br/>
[<b>‑negative_gilist</b> filename]<br/>
[<b>‑entrez_query</b> entrez_query]<br/>
[<b>‑db_soft_mask</b> filtering_algorithm]<br/>
[<b>‑db_hard_mask</b> filtering_algorithm]<br/>
[<b>‑subject</b> subject_input_file]<br/>
[<b>‑subject_loc</b> range]<br/>
[<b>‑query</b> input_file]<br/>
[<b>‑out</b> output_file]<br/>
[<b>‑evalue</b> evalue]<br/>
[<b>‑word_size</b> int_value]<br/>
[<b>‑gapopen</b> open_penalty]<br/>
[<b>‑gapextend</b> extend_penalty]<br/>
[<b>‑perc_identity</b> float_value]<br/>
[<b>‑qcov_hsp_perc</b> float_value]<br/>
[<b>‑max_hsps</b> int_value]<br/>
[<b>‑xdrop_ungap</b> float_value]<br/>
[<b>‑xdrop_gap</b> float_value]<br/>
[<b>‑xdrop_gap_final</b> float_value]<br/>
[<b>‑searchsp</b> int_value]<br/>
[<b>‑sum_stats</b> bool_value]<br/>
[<b>‑penalty</b> penalty]<br/>
[<b>‑reward</b> reward]<br/>
[<b>‑no_greedy</b>]<br/>
[<b>‑min_raw_gapped_score</b> int_value]<br/>
[<b>‑template_type</b> type]<br/>
[<b>‑template_length</b> int_value]<br/>
[<b>‑dust</b> DUST_options]<br/>
[<b>‑filtering_db</b> filtering_database]<br/>
[<b>‑window_masker_taxid</b> window_masker_taxid]<br/>
[<b>‑window_masker_db</b> window_masker_db]<br/>
[<b>‑soft_masking</b> soft_masking]<br/>
[<b>‑ungapped</b>]<br/>
[<b>‑culling_limit</b> int_value]<br/>
[<b>‑best_hit_overhang</b> float_value]<br/>
[<b>‑best_hit_score_edge</b> float_value]<br/>
[<b>‑window_size</b> int_value]<br/>
[<b>‑off_diagonal_range</b> int_value]<br/>
[<b>‑use_index</b> boolean]<br/>
[<b>‑index_name</b> string]<br/>
[<b>‑lcase_masking</b>]<br/>
[<b>‑query_loc</b> range]<br/>
[<b>‑strand</b> strand]<br/>
[<b>‑parse_deflines</b>]<br/>
[<b>‑outfmt</b> format]<br/>
[<b>‑show_gis</b>]<br/>
[<b>‑num_descriptions</b> int_value]<br/>
[<b>‑num_alignments</b> int_value]<br/>
[<b>‑line_length</b> line_length]<br/>
[<b>‑html</b>]<br/>
[<b>‑max_target_seqs</b> num_sequences]<br/>
[<b>‑num_threads</b> int_value]<br/>
[<b>‑remote</b>]<br/>
[<b>‑version</b>]<span style="float:right"><a href="#top">TOP</a></span>
</div>
<hr style="background-image: linear-gradient(to right, white, blue, white); color: blue; height: 1px; border: 0;"/>
<h4 style="text-align:center; color:blue;" id="blastp">BlastP - Commandline Parameters</h4>
<div style="padding: 0 15px 0 15px;">
blastp [<b>‑h</b>] [<b>‑help</b>]<br/>
[<b>‑import_search_strategy</b> filename]<br/>
[<b>‑export_search_strategy</b> filename]<br/>
[<b>‑task</b> task_name]<br/>
[<b>‑db</b> database_name]<br/>
[<b>‑dbsize</b> num_letters]<br/>
[<b>‑gilist</b> filename]<br/>
[<b>‑seqidlist</b> filename]<br/>
[<b>‑negative_gilist</b> filename]<br/>
[<b>‑entrez_query</b> entrez_query]<br/>
[<b>‑db_soft_mask</b> filtering_algorithm]<br/>
[<b>‑db_hard_mask</b> filtering_algorithm]<br/>
[<b>‑subject</b> subject_input_file]<br/>
[<b>‑subject_loc</b> range]<br/>
[<b>‑query</b> input_file]<br/>
[<b>‑out</b> output_file]<br/>
[<b>‑evalue</b> evalue]<br/>
[<b>‑word_size</b> int_value]<br/>
[<b>‑gapopen</b> open_penalty]<br/>
[<b>‑gapextend</b> extend_penalty]<br/>
[<b>‑qcov_hsp_perc</b> float_value]<br/>
[<b>‑max_hsps</b> int_value]<br/>
[<b>‑xdrop_ungap</b> float_value]<br/>
[<b>‑xdrop_gap</b> float_value]<br/>
[<b>‑xdrop_gap_final</b> float_value]<br/>
[<b>‑searchsp</b> int_value]<br/>
[<b>‑sum_stats</b> bool_value]<br/>
[<b>‑seg</b> SEG_options]<br/>
[<b>‑soft_masking</b> soft_masking]<br/>
[<b>‑matrix</b> matrix_name]<br/>
[<b>‑threshold</b> float_value]<br/>
[<b>‑culling_limit</b> int_value]<br/>
[<b>‑best_hit_overhang</b> float_value]<br/>
[<b>‑best_hit_score_edge</b> float_value]<br/>
[<b>‑window_size</b> int_value]<br/>
[<b>‑lcase_masking</b>]<br/>
[<b>‑query_loc</b> range]<br/>
[<b>‑parse_deflines</b>]<br/>
[<b>‑outfmt</b> format]<br/>
[<b>‑show_gis</b>]<br/>
[<b>‑num_descriptions</b> int_value]<br/>
[<b>‑num_alignments</b> int_value]<br/>
[<b>‑line_length</b> line_length]<br/>
[<b>‑html</b>]<br/>
[<b>‑max_target_seqs</b> num_sequences]<br/>
[<b>‑num_threads</b> int_value]<br/>
[<b>‑ungapped</b>]<br/>
[<b>‑remote</b>]<br/>
[<b>‑comp_based_stats</b> compo]<br/>
[<b>‑use_sw_tback</b>]<br/>
[<b>‑version</b>]<span style="float:right"><a href="#top">TOP</a></span>
</div>
<hr style="background-image: linear-gradient(to right, white, blue, white); color: blue; height: 1px; border: 0;"/>
<h4 style="text-align:center; color:blue;" id="blastx">BlastX - Commandline Parameters</h4>
<div style="padding: 0 15px 0 15px;">
blastx [<b>‑h</b>] [<b>‑help</b>]<br/>
[<b>‑import_search_strategy</b> filename]<br/>
[<b>‑export_search_strategy</b> filename]<br/>
[<b>‑task</b> task_name]<br/>
[<b>‑db</b> database_name]<br/>
[<b>‑dbsize</b> num_letters]<br/>
[<b>‑gilist</b> filename]<br/>
[<b>‑seqidlist</b> filename]<br/>
[<b>‑negative_gilist</b> filename]<br/>
[<b>‑entrez_query</b> entrez_query]<br/>
[<b>‑db_soft_mask</b> filtering_algorithm]<br/>
[<b>‑db_hard_mask</b> filtering_algorithm]<br/>
[<b>‑subject</b> subject_input_file]<br/>
[<b>‑subject_loc</b> range]<br/>
[<b>‑query</b> input_file]<br/>
[<b>‑out</b> output_file]<br/>
[<b>‑evalue</b> evalue]<br/>
[<b>‑word_size</b> int_value]<br/>
[<b>‑gapopen</b> open_penalty]<br/>
[<b>‑gapextend</b> extend_penalty]<br/>
[<b>‑qcov_hsp_perc</b> float_value]<br/>
[<b>‑max_hsps</b> int_value]<br/>
[<b>‑xdrop_ungap</b> float_value]<br/>
[<b>‑xdrop_gap</b> float_value]<br/>
[<b>‑xdrop_gap_final</b> float_value]<br/>
[<b>‑searchsp</b> int_value]<br/>
[<b>‑sum_stats</b> bool_value]<br/>
[<b>‑max_intron_length</b> length]<br/>
[<b>‑seg</b> SEG_options]<br/>
[<b>‑soft_masking</b> soft_masking]<br/>
[<b>‑matrix</b> matrix_name]<br/>
[<b>‑threshold</b> float_value]<br/>
[<b>‑culling_limit</b> int_value]<br/>
[<b>‑best_hit_overhang</b> float_value]<br/>
[<b>‑best_hit_score_edge</b> float_value]<br/>
[<b>‑window_size</b> int_value]<br/>
[<b>‑ungapped</b>]<br/>
[<b>‑lcase_masking</b>]<br/>
[<b>‑query_loc</b> range]<br/>
[<b>‑strand</b> strand]<br/>
[<b>‑parse_deflines</b>]<br/>
[<b>‑query_gencode</b> int_value]<br/>
[<b>‑outfmt</b> format]<br/>
[<b>‑show_gis</b>]<br/>
[<b>‑num_descriptions</b> int_value]<br/>
[<b>‑num_alignments</b> int_value]<br/>
[<b>‑line_length</b> line_length]<br/>
[<b>‑html</b>]<br/>
[<b>‑max_target_seqs</b> num_sequences]<br/>
[<b>‑num_threads</b> int_value]<br/>
[<b>‑remote</b>]<br/>
[<b>‑comp_based_stats</b> compo]<br/>
[<b>‑use_sw_tback</b>]<br/>
[<b>‑version</b>]<span style="float:right"><a href="#top">TOP</a></span>
</div>
<hr style="background-image: linear-gradient(to right, white, blue, white); color: blue; height: 1px; border: 0;"/>
<h4 style="text-align:center; color:blue;" id="tblastn">tBlastN - Commandline Parameters</h4>
<div style="padding: 0 15px 0 15px;">
tblastn [<b>‑h</b>] [<b>‑help</b>]<br/>
[<b>‑import_search_strategy</b> filename]<br/>
[<b>‑export_search_strategy</b> filename]<br/>
[<b>‑task</b> task_name]<br/>
[<b>‑db</b> database_name]<br/>
[<b>‑dbsize</b> num_letters]<br/>
[<b>‑gilist</b> filename]<br/>
[<b>‑seqidlist</b> filename]<br/>
[<b>‑negative_gilist</b> filename]<br/>
[<b>‑entrez_query</b> entrez_query]<br/>
[<b>‑db_soft_mask</b> filtering_algorithm]<br/>
[<b>‑db_hard_mask</b> filtering_algorithm]<br/>
[<b>‑subject</b> subject_input_file]<br/>
[<b>‑subject_loc</b> range]<br/>
[<b>‑query</b> input_file]<br/>
[<b>‑out</b> output_file]<br/>
[<b>‑evalue</b> evalue]<br/>
[<b>‑word_size</b> int_value]<br/>
[<b>‑gapopen</b> open_penalty]<br/>
[<b>‑gapextend</b> extend_penalty]<br/>
[<b>‑qcov_hsp_perc</b> float_value]<br/>
[<b>‑max_hsps</b> int_value]<br/>
[<b>‑xdrop_ungap</b> float_value]<br/>
[<b>‑xdrop_gap</b> float_value]<br/>
[<b>‑xdrop_gap_final</b> float_value]<br/>
[<b>‑searchsp</b> int_value]<br/>
[<b>‑sum_stats</b> bool_value]<br/>
[<b>‑db_gencode</b> int_value]<br/>
[<b>‑ungapped</b>]<br/>
[<b>‑max_intron_length</b> length]<br/>
[<b>‑seg</b> SEG_options]<br/>
[<b>‑soft_masking</b> soft_masking]<br/>
[<b>‑matrix</b> matrix_name]<br/>
[<b>‑threshold</b> float_value]<br/>
[<b>‑culling_limit</b> int_value]<br/>
[<b>‑best_hit_overhang</b> float_value]<br/>
[<b>‑best_hit_score_edge</b> float_value]<br/>
[<b>‑window_size</b> int_value]<br/>
[<b>‑lcase_masking</b>]<br/>
[<b>‑query_loc</b> range]<br/>
[<b>‑parse_deflines</b>]<br/>
[<b>‑outfmt</b> format]<br/>
[<b>‑show_gis</b>]<br/>
[<b>‑num_descriptions</b> int_value]<br/>
[<b>‑num_alignments</b> int_value]<br/>
[<b>‑line_length</b> line_length]<br/>
[<b>‑html</b>]<br/>
[<b>‑max_target_seqs</b> num_sequences]<br/>
[<b>‑num_threads</b> int_value]<br/>
[<b>‑remote</b>]<br/>
[<b>‑comp_based_stats</b> compo]<br/>
[<b>‑use_sw_tback</b>]<br/>
[<b>‑in_pssm</b> psi_chkpt_file]<br/>
[<b>‑version</b>]<span style="float:right"><a href="#top">TOP</a></span>
</div>
<hr style="background-image: linear-gradient(to right, white, blue, white); color: blue; height: 1px; border: 0;"/>
<h4 style="text-align:center; color:blue;" id="tblastx">tBlastX - Commandline Parameters</h4>
<div style="padding: 0 15px 0 15px;">
tblastx [<b>‑h</b>] [<b>‑help</b>]<br/>
[<b>‑import_search_strategy</b> filename]<br/>
[<b>‑export_search_strategy</b> filename]<br/>
[<b>‑db</b> database_name]<br/>
[<b>‑dbsize</b> num_letters]<br/>
[<b>‑gilist</b> filename]<br/>
[<b>‑seqidlist</b> filename]<br/>
[<b>‑negative_gilist</b> filename]<br/>
[<b>‑entrez_query</b> entrez_query]<br/>
[<b>‑db_soft_mask</b> filtering_algorithm]<br/>
[<b>‑db_hard_mask</b> filtering_algorithm]<br/>
[<b>‑subject</b> subject_input_file]<br/>
[<b>‑subject_loc</b> range]<br/>
[<b>‑query</b> input_file]<br/>
[<b>‑out</b> output_file]<br/>
[<b>‑evalue</b> evalue]<br/>
[<b>‑word_size</b> int_value]<br/>
[<b>‑qcov_hsp_perc</b> float_value]<br/>
[<b>‑max_hsps</b> int_value]<br/>
[<b>‑xdrop_ungap</b> float_value]<br/>
[<b>‑searchsp</b> int_value]<br/>
[<b>‑sum_stats</b> bool_value]<br/>
[<b>‑max_intron_length</b> length]<br/>
[<b>‑seg</b> SEG_options]<br/>
[<b>‑soft_masking</b> soft_masking]<br/>
[<b>‑matrix</b> matrix_name]<br/>
[<b>‑threshold</b> float_value]<br/>
[<b>‑culling_limit</b> int_value]<br/>
[<b>‑best_hit_overhang</b> float_value]<br/>
[<b>‑best_hit_score_edge</b> float_value]<br/>
[<b>‑window_size</b> int_value]<br/>
[<b>‑lcase_masking</b>]<br/>
[<b>‑query_loc</b> range]<br/>
[<b>‑strand</b> strand]<br/>
[<b>‑parse_deflines</b>]<br/>
[<b>‑query_gencode</b> int_value]<br/>
[<b>‑db_gencode</b> int_value]<br/>
[<b>‑outfmt</b> format]<br/>
[<b>‑show_gis</b>]<br/>
[<b>‑num_descriptions</b> int_value]<br/>
[<b>‑num_alignments</b> int_value]<br/>
[<b>‑line_length</b> line_length]<br/>
[<b>‑html</b>]<br/>
[<b>‑max_target_seqs</b> num_sequences]<br/>
[<b>‑num_threads</b> int_value]<br/>
[<b>‑remote</b>]<br/>
[<b>‑version</b>]<span style="float:right"><a href="#top">TOP</a></span>
</div>
<hr style="background-image: linear-gradient(to right, white, blue, white); color: blue; height: 1px; border: 0;"/>
<h4 style="text-align:center; color:blue;" id="deltablast">DeltaBlast - Commandline Parameters</h4>
<div style="padding: 0 15px 0 15px;">
deltablast [<b>‑h</b>] [<b>‑help</b>]<br/>
[<b>‑import_search_strategy</b> filename]<br/>
[<b>‑export_search_strategy</b> filename]<br/>
[<b>‑db</b> database_name]<br/>
[<b>‑dbsize</b> num_letters]<br/>
[<b>‑gilist</b> filename]<br/>
[<b>‑seqidlist</b> filename]<br/>
[<b>‑negative_gilist</b> filename]<br/>
[<b>‑entrez_query</b> entrez_query]<br/>
[<b>‑subject</b> subject_input_file]<br/>
[<b>‑subject_loc</b> range]<br/>
[<b>‑query</b> input_file]<br/>
[<b>‑out</b> output_file]<br/>
[<b>‑evalue</b> evalue]<br/>
[<b>‑word_size</b> int_value]<br/>
[<b>‑gapopen</b> open_penalty]<br/>
[<b>‑gapextend</b> extend_penalty]<br/>
[<b>‑qcov_hsp_perc</b> float_value]<br/>
[<b>‑max_hsps</b> int_value]<br/>
[<b>‑xdrop_ungap</b> float_value]<br/>
[<b>‑xdrop_gap</b> float_value]<br/>
[<b>‑xdrop_gap_final</b> float_value]<br/>
[<b>‑searchsp</b> int_value]<br/>
[<b>‑sum_stats</b> bool_value]<br/>
[<b>‑seg</b> SEG_options]<br/>
[<b>‑soft_masking</b> soft_masking]<br/>
[<b>‑matrix</b> matrix_name]<br/>
[<b>‑threshold</b> float_value]<br/>
[<b>‑culling_limit</b> int_value]<br/>
[<b>‑best_hit_overhang</b> float_value]<br/>
[<b>‑best_hit_score_edge</b> float_value]<br/>
[<b>‑window_size</b> int_value]<br/>
[<b>‑lcase_masking</b>]<br/>
[<b>‑query_loc</b> range]<br/>
[<b>‑parse_deflines</b>]<br/>
[<b>‑outfmt</b> format]<br/>
[<b>‑show_gis</b>]<br/>
[<b>‑num_descriptions</b> int_value]<br/>
[<b>‑num_alignments</b> int_value]<br/>
[<b>‑line_length</b> line_length]<br/>
[<b>‑html</b>]<br/>
[<b>‑max_target_seqs</b> num_sequences]<br/>
[<b>‑num_threads</b> int_value]<br/>
[<b>‑remote</b>]<br/>
[<b>‑comp_based_stats</b> compo]<br/>
[<b>‑use_sw_tback</b>]<br/>
[<b>‑gap_trigger</b> float_value]<br/>
[<b>‑num_iterations</b> int_value]<br/>
[<b>‑out_pssm</b> checkpoint_file]<br/>
[<b>‑out_ascii_pssm</b> ascii_mtx_file]<br/>
[<b>‑save_pssm_after_last_round</b>]<br/>
[<b>‑save_each_pssm</b>]<br/>
[<b>‑pseudocount</b> pseudocount]<br/>
[<b>‑domain_inclusion_ethresh</b> ethresh]<br/>
[<b>‑inclusion_ethresh</b> ethresh]<br/>
[<b>‑rpsdb</b> database_name]<br/>
[<b>‑show_domain_hits</b>]<br/>
[<b>‑version</b>]<span style="float:right"><a href="#top">TOP</a></span>
</div>
<hr style="background-image: linear-gradient(to right, white, blue, white); color: blue; height: 1px; border: 0;"/>
<h4 style="text-align:center; color:blue;" id="psiblast">PSI-Blast - Commandline Parameters</h4>
<div style="padding: 0 15px 0 15px;">
psiblast [<b>‑h</b>] [<b>‑help</b>]<br/>
[<b>‑import_search_strategy</b> filename]<br/>
[<b>‑export_search_strategy</b> filename]<br/>
[<b>‑db</b> database_name]<br/>
[<b>‑dbsize</b> num_letters]<br/>
[<b>‑gilist</b> filename]<br/>
[<b>‑seqidlist</b> filename]<br/>
[<b>‑negative_gilist</b> filename]<br/>
[<b>‑entrez_query</b> entrez_query]<br/>
[<b>‑subject</b> subject_input_file]<br/>
[<b>‑subject_loc</b> range]<br/>
[<b>‑query</b> input_file]<br/>
[<b>‑out</b> output_file]<br/>
[<b>‑evalue</b> evalue]<br/>
[<b>‑word_size</b> int_value]<br/>
[<b>‑gapopen</b> open_penalty]<br/>
[<b>‑gapextend</b> extend_penalty]<br/>
[<b>‑qcov_hsp_perc</b> float_value]<br/>
[<b>‑max_hsps</b> int_value]<br/>
[<b>‑xdrop_ungap</b> float_value]<br/>
[<b>‑xdrop_gap</b> float_value]<br/>
[<b>‑xdrop_gap_final</b> float_value]<br/>
[<b>‑searchsp</b> int_value]<br/>
[<b>‑sum_stats</b> bool_value]<br/>
[<b>‑seg</b> SEG_options]<br/>
[<b>‑soft_masking</b> soft_masking]<br/>
[<b>‑matrix</b> matrix_name]<br/>
[<b>‑threshold</b> float_value]<br/>
[<b>‑culling_limit</b> int_value]<br/>
[<b>‑best_hit_overhang</b> float_value]<br/>
[<b>‑best_hit_score_edge</b> float_value]<br/>
[<b>‑window_size</b> int_value]<br/>
[<b>‑lcase_masking</b>]<br/>
[<b>‑query_loc</b> range]<br/>
[<b>‑parse_deflines</b>]<br/>
[<b>‑outfmt</b> format]<br/>
[<b>‑show_gis</b>]<br/>
[<b>‑num_descriptions</b> int_value]<br/>
[<b>‑num_alignments</b> int_value]<br/>
[<b>‑line_length</b> line_length]<br/>
[<b>‑html</b>]<br/>
[<b>‑max_target_seqs</b> num_sequences]<br/>
[<b>‑num_threads</b> int_value]<br/>
[<b>‑remote</b>]<br/>
[<b>‑comp_based_stats</b> compo]<br/>
[<b>‑use_sw_tback</b>]<br/>
[<b>‑gap_trigger</b> float_value]<br/>
[<b>‑num_iterations</b> int_value]<br/>
[<b>‑out_pssm</b> checkpoint_file]<br/>
[<b>‑out_ascii_pssm</b> ascii_mtx_file]<br/>
[<b>‑save_pssm_after_last_round</b>]<br/>
[<b>‑save_each_pssm</b>]<br/>
[<b>‑in_msa</b> align_restart]<br/>
[<b>‑msa_master_idx</b> index]<br/>
[<b>‑ignore_msa_master</b>]<br/>
[<b>‑in_pssm</b> psi_chkpt_file]<br/>
[<b>‑pseudocount</b> pseudocount]<br/>
[<b>‑inclusion_ethresh</b> ethresh]<br/>
[<b>‑phi_pattern</b> file]<br/>
[<b>‑version</b>]<span style="float:right"><a href="#top">TOP</a></span>
</div>
<hr style="background-image: linear-gradient(to right, white, blue, white); color: blue; height: 1px; border: 0;"/>
<h4 style="text-align:center; color:blue;" id="rpsblast">RPS-Blast - Commandline Parameters</h4>
<div style="padding: 0 15px 0 15px;">
rpsblast [<b>‑h</b>] [<b>‑help</b>]<br/>
[<b>‑import_search_strategy</b> filename]<br/>
[<b>‑export_search_strategy</b> filename]<br/>
[<b>‑db</b> database_name]<br/>
[<b>‑dbsize</b> num_letters]<br/>
[<b>‑entrez_query</b> entrez_query]<br/>
[<b>‑query</b> input_file]<br/>
[<b>‑out</b> output_file]<br/>
[<b>‑evalue</b> evalue]<br/>
[<b>‑qcov_hsp_perc</b> float_value]<br/>
[<b>‑max_hsps</b> int_value]<br/>
[<b>‑xdrop_ungap</b> float_value]<br/>
[<b>‑xdrop_gap</b> float_value]<br/>
[<b>‑xdrop_gap_final</b> float_value]<br/>
[<b>‑searchsp</b> int_value]<br/>
[<b>‑sum_stats</b> bool_value]<br/>
[<b>‑seg</b> SEG_options]<br/>
[<b>‑soft_masking</b> soft_masking]<br/>
[<b>‑culling_limit</b> int_value]<br/>
[<b>‑best_hit_overhang</b> float_value]<br/>
[<b>‑best_hit_score_edge</b> float_value]<br/>
[<b>‑window_size</b> int_value]<br/>
[<b>‑lcase_masking</b>]<br/>
[<b>‑query_loc</b> range]<br/>
[<b>‑parse_deflines</b>]<br/>
[<b>‑outfmt</b> format]<br/>
[<b>‑show_gis</b>]<br/>
[<b>‑num_descriptions</b> int_value]<br/>
[<b>‑num_alignments</b> int_value]<br/>
[<b>‑line_length</b> line_length]<br/>
[<b>‑html</b>]<br/>
[<b>‑max_target_seqs</b> num_sequences]<br/>
[<b>‑num_threads</b> int_value]<br/>
[<b>‑remote</b>]<br/>
[<b>‑comp_based_stats</b> compo]<br/>
[<b>‑use_sw_tback</b>]<br/>
[<b>‑version</b>]<span style="float:right"><a href="#top">TOP</a></span>
</div>
<hr style="background-image: linear-gradient(to right, white, blue, white); color: blue; height: 1px; border: 0;"/>
<h4 style="text-align:center; color:blue;" id="rpstblastn">RPS-tBlastN - Commandline Parameters</h4>
<div style="padding: 0 15px 0 15px;">
rpstblastn [<b>‑h</b>] [<b>‑help</b>]<br/>
[<b>‑import_search_strategy</b> filename]<br/>
[<b>‑export_search_strategy</b> filename]<br/>
[<b>‑db</b> database_name]<br/>
[<b>‑dbsize</b> num_letters]<br/>
[<b>‑entrez_query</b> entrez_query]<br/>
[<b>‑query</b> input_file]<br/>
[<b>‑out</b> output_file]<br/>
[<b>‑evalue</b> evalue]<br/>
[<b>‑qcov_hsp_perc</b> float_value]<br/>
[<b>‑max_hsps</b> int_value]<br/>
[<b>‑xdrop_ungap</b> float_value]<br/>
[<b>‑xdrop_gap</b> float_value]<br/>
[<b>‑xdrop_gap_final</b> float_value]<br/>
[<b>‑searchsp</b> int_value]<br/>
[<b>‑sum_stats</b> bool_value]<br/>
[<b>‑query_gencode</b> int_value]<br/>
[<b>‑seg</b> SEG_options]<br/>
[<b>‑soft_masking</b> soft_masking]<br/>
[<b>‑window_size</b> int_value]<br/>
[<b>‑ungapped</b>]<br/>
[<b>‑lcase_masking</b>]<br/>
[<b>‑query_loc</b> range]<br/>
[<b>‑strand</b> strand]<br/>
[<b>‑parse_deflines</b>]<br/>
[<b>‑outfmt</b> format]<br/>
[<b>‑show_gis</b>]<br/>
[<b>‑num_descriptions</b> int_value]<br/>
[<b>‑num_alignments</b> int_value]<br/>
[<b>‑line_length</b> line_length]<br/>
[<b>‑html</b>]<br/>
[<b>‑max_target_seqs</b> num_sequences]<br/>
[<b>‑num_threads</b> int_value]<br/>
[<b>‑remote</b>]<br/>
[<b>‑comp_based_stats</b> compo]<br/>
[<b>‑use_sw_tback</b>]<br/>
[<b>‑version</b>]<span style="float:right"><a href="#top">TOP</a></span>
</div>
</div>
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