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 | 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 | Description |
---|---|---|
class |
IUPACPenaltyTable |
Implements a table of transition penalties for a DNA states
and IUPAC ambiguous states.
|