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- MatrixDelta - class in org.veupathdb.lib.blast.deltablast.fields
- -matrix
<String>Scoring matrix name (normally BLOSUM62) - MatrixDeltaType - class in org.veupathdb.lib.blast.deltablast.fields
- MatrixPSI - class in org.veupathdb.lib.blast.psiblast.fields
- -matrix
<String>Scoring matrix name (normally BLOSUM62) - MatrixPSIType - class in org.veupathdb.lib.blast.psiblast.fields
- MaxHSPs - class in org.veupathdb.lib.blast.common.fields
- -max_hsps
<Integer, >=1>Set maximum number of HSPs per subject sequence to save for each query. - MaxIntronLength - class in org.veupathdb.lib.blast.common.fields
- -max_intron_length
<Integer, >=0>Length of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignmentsDefault =0 - MaxTargetSeqs - class in org.veupathdb.lib.blast.common.fields
- -max_target_seqs
<Integer, >=1>Maximum number of aligned sequences to keep (value of 5 or more is recommended)Default =500 - Megablast - enum entry in org.veupathdb.lib.blast.blastn.fields.BlastNTaskType
- MinRawGappedScore - class in org.veupathdb.lib.blast.blastn.fields
- -min_raw_gapped_score
<Integer>Minimum raw gapped score to keep an alignment in the preliminary gapped and traceback stages - Minus - enum entry in org.veupathdb.lib.blast.common.fields.StrandType
- MSAMasterIndex - class in org.veupathdb.lib.blast.psiblast.fields
- -msa_master_idx
<Integer, >=1>Ordinal number (1-based index) of the sequence to use as a master in the multiple sequence alignment. - MultipleFileBlastJSON - enum entry in org.veupathdb.lib.blast.common.fields.FormatType
- MultipleFileBlastXML2 - enum entry in org.veupathdb.lib.blast.common.fields.FormatType
- MultiThreadingMode - class in org.veupathdb.lib.blast.common.fields
- -mt_mode
<Integer, (>=0 and =<1)>Multi-thread mode to use in RPS BLAST search:0 (auto) split by database vols
1 split by queries
0 - MultiThreadingModeValue - class in org.veupathdb.lib.blast.common.fields