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: //www.phylosoft.org/NHX/nhx.pdf
This document is available at: //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.
(((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];
| 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 |
phyloXML website: //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: //evolution.genetics.washington.edu/phylip/newicktree.html
PHYLIP: //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
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Last updated 2008.04.15