distance

Documentation

Index

• func JCDist(dna1 seq.DNA, dna2 seq.DNA) float64
• func K80Dist(dna1 seq.DNA, dna2 seq.DNA) float64
• func PDist(dna1 seq.DNA, dna2 seq.DNA) float64
• func PrettyPrintDist(dmat DistMat)
• func PrettySaveDist(dmat DistMat, path string, name string)
• type DistMat
  • func PairDist(pool seq.DNAPool, method string) DistMat
  • func PairDistConc(pool seq.DNAPool, model string) DistMat

Functions

func JCDist

func JCDist(dna1 seq.DNA, dna2 seq.DNA) float64

JCDist calculates Jukes-Cantor distance between two sequences

func K80Dist

func K80Dist(dna1 seq.DNA, dna2 seq.DNA) float64

K80Dist calculates Kimure-Nei distance between two sequences

func PDist

func PDist(dna1 seq.DNA, dna2 seq.DNA) float64

PDist calculates p-distance between two sequences

func PrettyPrintDist

func PrettyPrintDist(dmat DistMat)

PrettyPrintDist prints a distance matrix to the stdout in a nice table format.

func PrettySaveDist

func PrettySaveDist(dmat DistMat, path string, name string)

PrettySaveDist saves a distance matrix in the disk in a nice table format.

Types

type DistMat

type DistMat struct {
	Ids       []string
	Matrix    [][]float64
	Method    string
	Alignment *seq.DNAPool
}

DistMat is a distance matrix structure

func PairDist

func PairDist(pool seq.DNAPool, method string) DistMat

PairDist calculates pairwise distances between all sequences in a DNAPool using the specified method (OLD).

func PairDistConc

func PairDistConc(pool seq.DNAPool, model string) DistMat

PairDistConc concurrently calculates the pairwise distances betwen all sequences in a DNAPool using the specified method.