NHX - New Hampshire eXtended [version 2.0]

Copyright (C) 1999 - 2009 by Christian M. Zmasek. Written by Christian M. Zmasek. Permission is granted to copy this document provided that this copyright notice is not removed and that the contents of this document are not altered in any way.

Download this document in PDF format at: http://www.phylosoft.org/NHX/nhx.pdf

This document is available at: http://www.phylosoft.org/NHX

Notice. This (version 2.0) is expected to be the final version of NHX.
It is recommended to use phyloXML (see: www.phyloxml.org) instead of NHX.

NHX is a format for describing annotated phylogenies. NHX is based on the New Hampshire (NH) standard (also called "Newick tree format"). It has the following extensions (compared to NH as used in the PHYLIP package):

In order to remain compatible with the NEXUS format, all fields except name and branch length (in other words, all fields eXtending NH) must be wrapped by "[&&NHX"and"]".E.g."ADH1:0.11[&&NHX:S=human:E=1.1.1.1]".

The following characters can not be part of names: ( ) [ ] , : ; as well as white space.

An example of a (rooted) phylogeny in NHX

(((ADH2:0.1[&&NHX:S=human:E=1.1.1.1], ADH1:0.11[&&NHX:S=human:E=1.1.1.1]):0.05[&&NHX:S=Primates:E=1.1.1.1:D=Y:B=100], ADHY:0.1[&&NHX:S=nematode:E=1.1.1.1],ADHX:0.12[&&NHX:S=insect:E=1.1.1.1]):0.1[&&NHX:S=Metazoa:E=1.1.1.1:D=N], (ADH4:0.09[&&NHX:S=yeast:E=1.1.1.1],ADH3:0.13[&&NHX:S=yeast:E=1.1.1.1], ADH2:0.12[&&NHX:S=yeast:E=1.1.1.1],ADH1:0.11[&&NHX:S=yeast:E=1.1.1.1]):0.1 [&&NHX:S=Fungi])[&&NHX:E=1.1.1.1:D=N];

NHX version 2.0 elements

Element Type Description Corresponding phyloXML element (parent element in parentheses)
no tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED) <name>(<clade>)
: decimal branch length to parent node (MUST BE SECOND, IF ASSIGNED) <branch_length>(<clade>)
:GN= string gene name <name>(<sequence>)
:AC= string sequence accession <accession>(<sequence>)
:ND= string node identifier - if this is being used, it has to be unique within each phylogeny <node_id>(<clade>)
:B= decimal confidence value for parent branch <confidence>(<clade>)
:D= 'T', 'F', or '?' 'T' if this node represents a duplication event - 'F' if this node represents a speciation event, '?' if this node represents an unknown event (D= tag should be replaced by Ev= tag) n/a
:Ev=duplications>speciations>gene losses>event type>duplication type int int int string string event (replaces the =D tag), number of duplication, speciation, and gene loss events, type of event (transfer, fusion, root, unknown, other, speciation_duplication_loss, unassigned) <events>(<clade>)
:E= string EC number at this node <annotation>(<sequence>)
:Fu= string function at this node <annotation>(<sequence>)
:DS=protein-length>from>to>support>name>from>... int int int double string int ... domain structure at this node <domain_architecture>(<sequence>)
:S= string species name of the species/phylum at this node <scientific_name> (<taxonomy>)
:T= integer taxonomy ID of the species/phylum at this node <id>(<taxonomy>)
:W= integer width of parent branch <width>(<clade>)
:C=rrr.ggg.bbb integer.integer.integer color of parent branch <color>(<clade>)
:Co= 'Y' or 'N' collapse this node when drawing the tree (default is not to collapse) n/a
:XB= string custom data associated with a branch <property>(<clade>)
:XN= string custom data associated with a node <property>(<clade>)
:O= integer orthologous to this external node n/a
:SN= integer subtree neighbors n/a
:SO= integer super orthologous (no duplications on paths) to this external node n/a

References

phyloXML website: http://www.phyloxml.org/

phyloXML reference: Han MV and Zmasek CM (2009). phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10:356

New Hampshire format: http://evolution.genetics.washington.edu/phylip/newicktree.html

PHYLIP: http://evolution.genetics.washington.edu/phylip.html

NEXUS format: Maddison DR, Swofford DL and Maddison WP (1997) NEXUS: an extensible file format for systematic information. Systematic Biology 46 590-621

Last updated 2008.04.15

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