Crate light_phylogeny[][src]

light structures and functions for phylogeny

light_phylogeny is a set of structures and functions dedicated to reading, building, manipulating and displaying phylogenic trees, especially reconciled trees with speciation, duplication, loss and horizontal transfer events. Read newick, phyloXML and recPhyloXML files.

Structs

ArenaTree

Structure ArenaTree.

Config

Structure Config: drawing config.

Noeud

Structure Noeud.

Options

Structure Options: drawing options.

Enums

Event

enum of the possible events in a gene tree

Functions

add_child

Add a node to another node

check_is_rooted

Check if tree in newick format is rooted

draw_sptree_gntrees

Draw a svg pipe species tree and several gene trees inside it

draw_tree

Draw a svg simple tree

get_gtransfer

Get the transfers in a gene tree

lca

Send the index of the last common ancestor of 2 nodes

map_parasite_g2s

Map a reconciled species tree to a pipe species tree

map_parasite_s2g

Map a pipe species tree to a reconciled species tree

map_transfer

Map a transfert in gene tree to the species tree

move_child

Move a node from a parent node to another node

newick2tree

Fill an ArenaTree structure with the contents of a parentheses tree.

phyloxml_processing

Create a svg of the tree in phyloxml context

read_newick

Read a newick file and store the tree into ArenaTree structure

read_phyloxml

Read a phyloxml file and store the tree into a ArenaTree structure

read_recphyloxml

Read a recphyloxml file and store the species and gene trees into several ArenaTree structures

real_length

Transforms the tree into real branch length representation

recphyloxml_processing

Create a svg of the tree in recphyloxml context

reset_pos

Reset all positions x y xmod ymod of the tree

scale_heigth

Scaling tree height

scale_width

Scaling width height

summary

Display a short summary of each node of the tree