Package | Description |
---|---|
pal.alignment |
Classes dealing with sequence alignments, including methods for reading
and printing in several possible formats, as well as rearranging and
concatenating.
|
pal.datatype |
Classes describing data types (nucleotides, amino acids, codons, codon tables etc.)
|
Modifier and Type | Method and Description |
---|---|
static double |
AlignmentUtils.getAlignmentPenalty(Alignment a,
DataType dataType,
TransitionPenaltyTable penalties,
double gapCreation,
double gapExtension,
boolean local)
Returns total sum of pairs alignment distance using gap creation
and extension penalties and transition penalties as defined in the
TransitionPenaltyTable provided.
|
static double |
AlignmentUtils.getAlignmentPenalty(Alignment a,
TransitionPenaltyTable penalties,
double gapCreation,
double gapExtension)
Returns total sum of pairs alignment penalty using gap creation
and extension penalties and transition penalties in the
TransitionPenaltyTable provided.
|
Modifier and Type | Class and Description |
---|---|
class |
IUPACPenaltyTable
Implements a table of transition penalties for a DNA states
and IUPAC ambiguous states.
|