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- Identity - enum entry in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType
- IgnoreMSAMaster - class in org.veupathdb.lib.blast.psiblast.fields
- -ignore_msa_masterIgnore the master sequence when creating PSSMRequires: -in_msa
- ImportSearchStrategy - class in org.veupathdb.lib.blast.common.fields
- -import_search_strategy
<File_In>Search strategy to use - IncludeSequenceData - enum entry in org.veupathdb.lib.blast.common.fields.FormatField
- InclusionEValueThreshold - class in org.veupathdb.lib.blast.common.fields
- -inclusion_ethresh
<Real>E-value inclusion threshold for pairwise alignmentsDefault =0.002 - incompatible(BlastField,BlastField) - function in org.veupathdb.lib.blast.err.ErrorMap
- Tests flags that are incompatible with one another and appends errors for both incompatible flags when an entry in others has a non-default value.
- IndexName - class in org.veupathdb.lib.blast.blastn.fields
- -index_name
<String>MegaBLAST database index name (deprecated; use only for old style indices) - InMSAFile - class in org.veupathdb.lib.blast.psiblast.fields
- -in_msa
<File_In>File name of multiple sequence alignment to restart PSI-BLAST - InPSSMFile - class in org.veupathdb.lib.blast.common.fields
- -in_pssm
<File_In>PSI-BLAST checkpoint file - IPGList - class in org.veupathdb.lib.blast.common.fields
- -ipglist
<String>Restrict search of database to list of IPGs