Crate light_phylogeny[−][src]

Expand description

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

Structure ArenaTree.

Structure Config: drawing config.

Structure Noeud.

Structure Options: drawing options.

Enums

enum of the possible events in a gene tree

Functions

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 a svg simple tree

Get the transfers in a gene tree

Send the index of the last common ancestor of 2 nodes

Map gene trees to host tree

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 a transfert in gene tree to the species tree

map_transfer_mul

Move a node from a parent node to another node

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

phyloxml_processing

Create a svg of the tree in phyloxml context

Read a newick file and store the tree into ArenaTree structure

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

read_recphyloxml_multi

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

Transforms the tree into real branch length representation

recphyloxml_processing

Create a svg of the tree in recphyloxml context

Reset all positions x y xmod ymod of the tree

Scaling tree height

Scaling width height

Display a short summary of each node of the tree