phylotree

Documentation

Overview

Package phylotree implements a phylogenetic tree with TMRCA estimates.

Index

• type Clade
  • func NewFromFile(filename string) (*Clade, error)
  • func (c *Clade) AddSample(sample Sample)
  • func (c *Clade) AddSubclade(clade Clade)
  • func (c *Clade) String() string
  • func (c *Clade) Subclade(cladeName string) *Clade
  • func (c *Clade) TMRCAs() []float64
• type Sample
  • func (s *Sample) String() string

Types

type Clade

type Clade struct {
	// Text is the text line used in the text representation of the tree.
	Text  string
	TMRCA float64
	// SNP is the name of the first SNP that characterizes this clade.
	SNP       string
	Subclades []Clade
	Samples   []Sample
}

Clade represents a phylogenetic clade.

func NewFromFile

func NewFromFile(filename string) (*Clade, error)

NewFromFile parses a text file to create a tree. The return value Clade is the root node of the tree.

func (*Clade) AddSample

func (c *Clade) AddSample(sample Sample)

func (*Clade) AddSubclade

func (c *Clade) AddSubclade(clade Clade)

func (*Clade) String

func (c *Clade) String() string

func (*Clade) Subclade

func (c *Clade) Subclade(cladeName string) *Clade

Subclade returns the subclade that contains searchTerm.

func (*Clade) TMRCAs

func (c *Clade) TMRCAs() []float64

TMRCAs returns the TMRCAs for all new lineages.

type Sample

type Sample struct {
	// Text is the text line used in the text representation of the tree.
	Text string
	ID   string
}

Sample is line of text that represents a genetic sample from a single person.

func (*Sample) String

func (s *Sample) String() string