PB Screw formats - mendessoares/BuddySuite GitHub Wiki

--screw_formats, -sf

Description

Convert the trees in one file format to another file format. Currently, NEXUS, Newick, and NeXML are supported.

Example

Input file: alpha_tree.nwk

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

Usage example

$: pb alpha_tree.nwk -sf nexus

Output

#NEXUS

BEGIN TAXA;
    DIMENSIONS NTAX=6;
    TAXLABELS
        A
        B
        C
        D
        E
        F
  ;
END;

BEGIN TREES;
    TREE 1 = ((A:1.0,(B:1.0,C:1.0):1.0):1.0,(D:1.0,E:1.0):1.0):1.0;
    TREE 2 = (((A:1.0,B:1.0):1.0,C:1.0):1.0,(D:1.0,E:1.0,F:1.0):1.0):1.0;
END;