NexusMetacommentFormat

Introduction

This is a brief description of the 'metacomment' format used by BEAST to annotate elements in the standard NEXUS format. This additional information is put in comments so that existing programs should read and ignore them.

Metacomments in trees

The standard format is:

<node>:<branch_length>

Where <node> can be a tip label or a subtree:

"tip1:0.01" or "(<node>:<branch_length>, <node>:<branch_length>):0.01"

Attributes make use of the comment feature of the NEXUS format (a comment is enclosed in square brackets). More specifically, [&<attribute>] is used with the ampersand denoting "metadata".

Node attributes are put before the colon:

<node>[&height=100.0]:<branch_length>

Branch attribute are put after the colon:

<node>:[&bootstrap=75.0]<branch_length>

The general form is [&<name>=<value>,<name>=<value>,...]

where <name> is a token and value is a number, a token (i.e., "true" or "red"), a quoted string or a list of values. Lists of values are given as:

<name>={<value>,<value>,..}

Some examples

[&colour={<colour1>,<time1>,<colour2>,<time2>,<colour3>}]

tip1:[&colour={<0>,<8.0>,<1>,<12.0>,<0>}] 20.0

This is a branch annotation with the colour starting at the time as 0, changing to 1 at time 8.0, reverting to 0 at time 12.0 and then remaining that colour up to time 20.0 (the total length of the branch).

A regex to match these is ("[^"]*"+|[^,=\s]+)\s*(=\s*(\{[^=}]*\}|"[^"]*"+|[^,]+))?