NEXUS file format - Revision history

Christoph at 04:55, 13 September 2006

2006-09-13T04:55:07Z

Christoph: Format +Cat

2005-12-30T20:08:38Z

Format +Cat

Christoph: Added another (simple) example + format

2005-12-28T19:35:31Z

Added another (simple) example + format

Christoph: /* Syntactic structure */ Added more tables, info., etc.

2005-12-28T19:16:53Z

‎Syntactic structure: Added more tables, info., etc.

Christoph: /* External links */ +link

2005-12-28T18:17:12Z

‎External links: +link

Christoph: /* Syntactic structure */ Added more "public blocks" to the table

2005-12-28T18:13:37Z

‎Syntactic structure: Added more "public blocks" to the table

Christoph: /* Orginial example (from paper) */ note about code

2005-12-28T18:02:16Z

‎Orginial example (from paper): note about code

Christoph: Added "clear=all"

2005-12-28T17:50:30Z

Added "clear=all"

Christoph: /* Example NEXUS files */ "Original example (from paper)"

2005-12-27T20:46:11Z

‎Example NEXUS files: "Original example (from paper)"

Christoph: /* Example NEXUS files */ Added "Basic" example

2005-12-27T20:27:47Z

‎Example NEXUS files: Added "Basic" example

@@ Line 496: / Line 496: @@
 * [http://en.wikipedia.org/wiki/Cladogram Wikipedia article on '''cladogram''']
-[[Category:Academic Research]]
+{{Phylogenetics}}
 [[Category:Phylogenetics]]

@@ Line 1: / Line 1: @@
-'''NEXUS''' is the file format used by many popular programs like GDA, Paup*, Mesquite, ModelTest, '''[[MrBayes]]''', and MacClade. Nexus file names often have a .nxs or .nex extension.
+'''NEXUS''' is the file format used by many popular programs like GDA, Paup*, Mesquite, ModelTest, '''[[MrBayes]]''', and MacClade. Nexus file names often have a <tt>.nxs</tt> or <tt>.nex</tt> extension.
-The NEXUS format conveys data organized according to the character state data model, in which the features of operational taxonomic units (OTUs) (e.g., species, individuals, genes, genomes, etc.) are observable states of underlying homologous characters. For instance, in a protein sequence alignment, proteins are the OTUs, alignment columns are characters, and amino acids (or gaps) are states. In evolutionary analysis, it is typical to consider differences as the result of state transitions that take place on branches of a tree, therefore the NEXUS file provides a means to represent a tree (in the standard Newick (a.k.a. New Hampshire) format).
+The NEXUS format conveys data organized according to the character state data model, in which the features of operational taxonomic units (OTUs) (e.g., species, individuals, genes, genomes, etc.) are observable states of underlying homologous characters. For instance, in a protein sequence alignment, proteins are the OTUs, alignment columns are characters, and [[amino acid]]s (or gaps) are states. In evolutionary analysis, it is typical to consider differences as the result of state transitions that take place on branches of a tree, therefore the NEXUS file provides a means to represent a tree (in the standard Newick (a.k.a. New Hampshire) format).
-==Syntactic structure==
+== Syntactic structure ==
 The syntactic structure of a '''NEXUS file''' is as follows:
@@ Line 136: / Line 136: @@
 <br clear="all" />
-===<tt>Format</tt> subcommands===
+=== <tt>Format</tt> subcommands ===
 The following are possible formatting subcommands:
@@ Line 153: / Line 153: @@
 * <tt>[No]Tokens</tt>
-===NEXUS Objects===
+=== NEXUS Objects ===
 Many of the commands in a NEXUS file define objects or specify characteristics about them. All objects can be labeled (given names). Duplicate names should be avoided as should names that differ only in case.
@@ Line 174: / Line 174: @@
 ; Definition list : list of definitions
-==Example Trees==
+== Example Trees ==
 Two character state trees and the NEXUS commands that define them. The first tree has an unnamed state.
@@ Line 194: / Line 194: @@
 </pre>
-==Example NEXUS files==
+== Example NEXUS files ==
-===Basic===
+=== Basic ===
 <pre>
 #NEXUS
@@ Line 488: / Line 488: @@
 </pre>
-==References==
+== References ==
-* Maddison DR, Swofford DL, and Maddison WP (1997). NEXUS: An extensible file format for systematic information. ''Syst. Biol.'' '''46''':590-621. ([http://workshop.molecularevolution.org/resources/references/files/maddison_et_al_1997.pdf PDF])
+* Maddison DR, Swofford DL, and Maddison WP (1997). NEXUS: An extensible file format for systematic information. ''Syst Biol'' '''46''':590-621. ([http://workshop.molecularevolution.org/resources/references/files/maddison_et_al_1997.pdf PDF])
-==External links==
+== External links ==
 * [http://www.molevol.org/camel/projects/nexus/ molevol.org - NEXUS]
 * [http://tolweb.org/nexus/ Some NEXUS information]
@@ Line 497: / Line 497: @@
 [[Category:Academic Research]]

@@ Line 4: / Line 4: @@
 ==Syntactic structure==
-The syntactic structure of a <smallcap>NEXUS</smallcap> file is as follows:
+The syntactic structure of a '''NEXUS file''' is as follows:
 <pre>
@@ Line 173: / Line 173: @@
 ; Definition list : list of definitions
 ==Example NEXUS files==
@@ Line 201: / Line 221: @@
 </pre>
-===Orginial example (from paper)===
+=== Simple example (orginal from paper) ===
 ''note: block names in bold (<nowiki><b></nowiki>); commands underlined (<nowiki><u></nowiki>).''
 <pre>
@@ Line 250: / Line 293: @@
 ===DNA===
 <pre>
-#nexus
+#NEXUS
-begin data;
+BEGIN DATA;
-dimensions ntax=10 nchar=705;
+        Dimensions NTax=10 NChar=705;
-format datatype=dna interleave=yes gap=- missing=?;
+        Format DataType=DNA Interleave=yes Gap=- Missing=?;
-matrix
+        Matrix
-Cow     ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA
+Cow     ATGGC ATATC CCATA CAACT AGGAT TCCAA GATGC AACAT CACCA ATCAT AGAAG AACTA
 Carp    ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT
 Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC
@@ Line 387: / Line 430: @@
 Frog    AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA
+;
-end;
+END;
 </pre>
@@ Line 451: / Line 494: @@
 * [http://www.molevol.org/camel/projects/nexus/ molevol.org - NEXUS]
 * [http://tolweb.org/nexus/ Some NEXUS information]
 [[Category:Academic Research]]

@@ Line 4: / Line 4: @@
 ==Syntactic structure==
-The syntactic structure of a NEXUS file is as follows:
+The syntactic structure of a <smallcap>NEXUS</smallcap> file is as follows:
 <pre>
@@ Line 13: / Line 13: @@
 end;
 [ < another block with commands > ]
 </pre>
@@ Line 20: / Line 43: @@
 {| align="center" style="border: 1px solid #999; background-color:#FFFFFF"
 |-
-! colspan="4" bgcolor="#EFEFEF" | '''Some important public blocks'''
+! colspan="2" bgcolor="#EFEFEF" | '''Some important public blocks'''
 |-align="center" bgcolor="#1188ee"
 !Name
@@ Line 31: / Line 54: @@
 |SETS || assigns names to sets of characters or OTUs
 |--bgcolor="#eeeeee"
-|ASSUMPTIONS || specifies assumptions for an analysis
+|ASSUMPTIONS || houses assumptions about the data or gives general directions as to how to treat them (e.g., which characters are to be excluded from consideration)
 |-
 |CODONS || specifies codons and their genetic codes
 |--bgcolor="#eeeeee"
-|DATA ||
+|DATA || equivalent to a <tt>CHARACTERS</tt> block in which the <tt>NewTaxa</tt> subcommand is included in the <tt>Dimensions</tt> command
 |-
-|TREES ||
+|TREES || stores information about trees
 |--bgcolor="#eeeeee"
 |UNALIGNED ||
 |-
-|DISTANCES ||
+|DISTANCES || contains distance matrices
 |--bgcolor="#eeeeee"
-|SETS ||
+|SETS || stores sets of objects (characters, states, taxa, etc.)
 |}
-<div align="center">''Source: [http://www.molevol.org/camel/projects/nexus/ molevol.org]''</div>
+<div align="center">''source: Maddison et al., 1997''</div>
 </div>
 <br clear="all" />
 ==Example NEXUS files==

@@ Line 325: / Line 325: @@
 ==External links==
 * [http://www.molevol.org/camel/projects/nexus/ molevol.org - NEXUS]
 [[Category:Academic Research]]

@@ Line 67: / Line 67: @@
 ===Orginial example (from paper)===
 <pre>
 BEGIN <b>TAXA</b>;

@@ Line 62: / Line 62: @@
 BEGIN TREES;
         tree "basic bush" = ((A:1,B:1):1,(C:1,D:1):1);
 END;
 </pre>

← Older revision		Revision as of 20:27, 27 December 2005
Line 39:		Line 39:

	==Example NEXUS files==		==Example NEXUS files==
		+
		+	===Basic===
		+	<pre>
		+	#NEXUS
		+
		+	BEGIN TAXA;
		+	dimensions ntax=4;
		+	taxlabels A B C D;
		+	END;
		+
		+	BEGIN CHARACTERS;
		+	dimensions nchar=5;
		+	format datatype=protein gap=-;
		+	charlabels 1 2 3 4 Five;
		+	matrix
		+	A MA-LL
		+	B MA-LE
		+	C MEATY
		+	D ME-TE
		+	END;
		+
		+	BEGIN TREES;
		+	tree "basic bush" = ((A:1,B:1):1,(C:1,D:1):1);
		+	END;
		+	</pre>

	===DNA===		===DNA===