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P

Pairwise - enum entry in org.veupathdb.lib.blast.common.fields.FormatType

 

Pam250 - enum entry in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType

 

Pam250 - enum entry in org.veupathdb.lib.blast.blastx.field.ScoringMatrixXType

 

Pam250 - enum entry in org.veupathdb.lib.blast.deltablast.fields.MatrixDeltaType

 

Pam250 - enum entry in org.veupathdb.lib.blast.psiblast.fields.MatrixPSIType

 

Pam250 - enum entry in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTNType

 

Pam250 - enum entry in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTXType

 

Pam30 - enum entry in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType

 

Pam30 - enum entry in org.veupathdb.lib.blast.blastx.field.ScoringMatrixXType

 

Pam30 - enum entry in org.veupathdb.lib.blast.deltablast.fields.MatrixDeltaType

 

Pam30 - enum entry in org.veupathdb.lib.blast.psiblast.fields.MatrixPSIType

 

Pam30 - enum entry in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTNType

 

Pam30 - enum entry in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTXType

 

Pam70 - enum entry in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType

 

Pam70 - enum entry in org.veupathdb.lib.blast.blastx.field.ScoringMatrixXType

 

Pam70 - enum entry in org.veupathdb.lib.blast.deltablast.fields.MatrixDeltaType

 

Pam70 - enum entry in org.veupathdb.lib.blast.psiblast.fields.MatrixPSIType

 

Pam70 - enum entry in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTNType

 

Pam70 - enum entry in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTXType

 

ParseDefLines - class in org.veupathdb.lib.blast.common.fields

-parse_deflinesShould the query and subject defline(s) be parsed?

Penalty - class in org.veupathdb.lib.blast.blastn.fields

-penalty <Integer, <=0>Penalty for a nucleotide mismatch

PercentageOfIdenticalMatches - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

 

PercentageOfPositiveScoringMatches - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

 

PercentIdentity - class in org.veupathdb.lib.blast.blastn.fields

-perc_identity <Real, 0..100>Percent identity

PHIPatternFile - class in org.veupathdb.lib.blast.psiblast.fields

-phi_pattern <File_In>File name containing pattern to search

Plus - enum entry in org.veupathdb.lib.blast.common.fields.StrandType

 

PseudoCount - class in org.veupathdb.lib.blast.common.fields

-pseudocount <Integer>Pseudo-count value used when constructing PSSMDefault = 0

psiblast(ObjectNode) - function in org.veupathdb.lib.blast.Blast

Creates a new PSIBlast instance by parsing the given JSON input.

psiblast() - function in org.veupathdb.lib.blast.Blast

Creates a new, defaulted PSIBlast instance.

PSIBlast - enum entry in org.veupathdb.lib.blast.BlastTool

 

PSIBlast - class in org.veupathdb.lib.blast.psiblast

Position-Specific Iterated BLAST 2.11.

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