garden/newick-format.md

Newick Format

• Format to represent trees with distances and branch names

Examples

Printed using DendroPY options show_internal_node_labels = True, width=40, plot_metric="length".

Single Descendant

(B)A;

A------------------------------------- B

Two Descendants

(B,C)A;

/------------------------------------- B
A
\------------------------------------- C

Two Levels Of Descendants

((D,E)B,(F,G)C)A;

                   /------------------ D
/------------------B
|                  \------------------ E
A
|                  /------------------ F
\------------------C
                   \------------------ G

Distances

(A:1,B:2);

/------------------ A
@
\------------------------------------- B

Big Example

(
    (
        (
            (
                Dasyatis_laosensis:0.00864712,
                Hemitrygon_akajei:0.02501331
            ):0.00555551,
            Dasyatis_sp._TT:0.01190329
        ):0.07844344,
        Maculabatis_gerrardi:0.10443933
    ):0.03362855,
    (
        Aetobatus_flagellum:0.06712780,
        (
            Aetobatus_narinari:0.00190402,
            Aetobatus_ocellatus:0.00159879
        ):0.05608476
    ):0.06364667,
    Squatina_squatina:0.24404039
);

         /Dasyatis laosensis
        /@
  /-----@\- Hemitrygon akajei
  |     |
/-@     \ Dasyatis sp. TT
| |
| \------- Maculabatis gerrardi
|
|   /----- Aetobatus flagellum
@---@
|   |    /Aetobatus narinari
|   \----@
|        \Aetobatus ocellatus
|
\------------------ Squatina squatina