NEXUS test set

The definitive version of this test file set is available at the NEXUS projects page on our web home. This HTML page is included with the test file set. If you are using a local copy, the version information is in your local file named VERSION.

To do the round-trip read test, you must install our NEXUS library. The test uses a simple script called test-rw-roundtrip.pl that carries out three operations:

read data from a NEXUS file into a nexus object in memory
write data from a nexus object in memory out to a NEXUS file
compare two nexus objects in memory

The file is read, written out, and re-read. The object read from the original file is then compared to the object read from the written-out file. The files cannot be UNIX-diff'ed because whitespace is irrelevant and the data include sets whose members have no specific order. The implementation of nexus object comparison uses block-specific methods to determine whether two blocks of the same type have the same content. So far, I have only seen one case where this method of testing fails to uncover an error (error reading branch lengths in sci notation in a tree). The plot test requires visual examination of the output to see that it makes sense. This is aided by using discretized branch lengths and other tricks that make it easier to determine if the content is being displayed correctly.

Some notes

NOTE: this includes some non-NEXUS files for conversion
NOTE: some of these files may be *non-conformant* or may use unsupported features. We will only support conformant files. Check the published format standard to determine conformance.
Files with a DATA block and no TAXA block are deprecated, but this format is so common we must support it for data input. To convert to the approved format, use
```
nextool.pl foo.nex foo-new.nex rewrite
```
to produce foo-new.nex with a TAXA block.
NOTE: many of these files represent real data gathered from scientific colleagues. We appreciate their help in providing this crucial resource. If the source of a data set is not listed here, look inside the file (and if it isn't there, please let us know so that we can give credit to our sources).

NEXUS files with imaginary character data and a taxa block

These files present various minor challenges such as comments, quoted strings, multiple trees, etc. They are all based on files with TAXA, CHARACTERS, and TREES blocks. Nearly all of them are derived from the basic-bush or basic-ladder file.

read	plot	Test	Description
pass	pass	basic-bush	symmetric bifurcating tree, all branch lengths = 1
pass	pass	basic-rake	basal polytomy, all branch lengths = 1
pass	pass	basic-ladder	maximally asymmetric tree, branch lengths = time
pass	pass	long-names	very long names in various places (OTU, char, tree labels)
fail	ND	quoted-strings1	OTU name "OTU C", charlabel "Char 3", tree name "the ladder tree"
fail	ND	quoted-strings2	OTU name 'OTU C', charlabel 'Char 3', tree name 'the ladder tree'
pass	pass	radical-whitespace	ridiculous but legal use of whitespace
fail	ND	top-level-comment	comment at the top level
pass	pass	intrablock-comment	comments within every block
pass	pass	multiline-intrablock-comment	multi-line comments within every block
pass	pass	char-matrix-spaces	char data are in blocks separated by spaces
pass	pass	char-interleave	char data are in interleaved format
pass	pass	trees-translate	bush tree with translated names
pass	pass	trees-tree-bush	basic bush
pass	pass	trees-tree-ladder	basic ladder
pass	pass	trees-tree-rake	basic rake
pass	pass	trees-tree-bush-cladogram	bush, no branch lengths
pass	pass	trees-tree-ladder-cladogram	ladder, no branch lengths
pass	pass	trees-tree-rake-cladogram	rake, no branch lengths
pass	pass	trees-tree-bush-quoted-string-name1	name of tree is "bush quoted string name1"
pass	pass	trees-tree-bush-quoted-string-name2	name of tree is 'bush quoted string name2'
pass	pass	trees-tree-bush-branchlength-zero	branch to OTU C with zero length
no!	ND	trees-tree-bush-branchlength-scientific	sci format for length of branches to OTU B (2e+01), C (9e-01), F (9E-01), G (2E+01)
pass	pass	trees-tree-bush-branchlength-negative	branch to CD ancestor with length = -0.25
pass	pass	trees-tree-bush-inode-labels	internal node labels
pass	pass	trees-tree-bush-inode-labels-partial	only some internal node labels
fail	ND	trees-tree-bush-inode-labels-quoted1	double quotation marks around inode labels
fail	ND	trees-tree-bush-inode-labels-quoted2	single quotation marks around inode labels
pass	pass	trees-tree-basal-trifurcation	basal trifurcation
pass	note	trees-tree-bush-extended-root-branch	bush with branch above root node
pass	note	trees-tree-multiple	trees "bush", "ladder" and "rake" in one trees block
warn	ND	trees-tree-multiple-challenges	one tree with each challenge above (see the treelist below)

the tree list

Trees are shown exactly as in the "tree" command in NEXUS trees block.

tree basal-trifurcation = (((A:1,B:1):1,(C:1,D:1):1):1,(E:1,F:1):2,(G:1,H:1):2);
tree bush = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
tree bush-branchlength-negative = (((A:1,B:1):1,(C:1,D:1):-0.25):1,((E:1,F:1):1,(G:1,H:1):1):1);
tree bush-branchlength-scientific = (((A:1,B:2e+01):1,(C:9e-01,D:1):1):1,((E:1,F:9E-01):1,(G:2E+01,H:1):1):1);
tree bush-branchlength-zero = (((A:1,B:1):1,(C:0,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
tree bush-cladogram = (((A,B),(C,D)),((E,F),(G,H)));
tree bush-extended-root-branch = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1):1;
tree bush-inode-labels = (((A:1,B:1)AB:1,(C:1,D:1)CD:1)ABCD:1,((E:1,F:1)EF:1,(G:1,H:1)GH:1)EFGH:1);
tree bush-inode-labels-partial = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1)EF:1,(G:1,H:1)GH:1)EFGH:1);
tree bush-inode-labels-quoted1 = (((A:1,B:1)"inode AB":1,(C:1,D:1)"inode CD":1)"inode ABCD":1,((E:1,F:1)"inode EF":1,(G:1,H:1)"inode GH":1)"inode EFGH":1);
tree bush-inode-labels-quoted2 = (((A:1,B:1)'inode AB':1,(C:1,D:1)'inode CD':1)'inode ABCD':1,((E:1,F:1)'inode EF':1,(G:1,H:1)'inode GH':1)'inode EFGH':1);
tree "bush quoted string name1" = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
tree 'bush quoted string name2' = (((A:1,B:1):1,(C:1,D:1):1):1,((E:1,F:1):1,(G:1,H:1):1):1);
tree bush-uneven = (((A:1,B:2):1,(C:1,D:2):1):1,((E:1,F:2):1,(G:1,H:2):1):1);
tree ladder = (((((((A:1,B:1):1,C:2):1,D:3):1,E:4):1,F:5):1,G:6):1,H:7);
tree ladder-cladogram = (((((((A,B),C),D),E),F),G),H);
tree ladder-uneven = (((((((A:1,B:2):1,C:2):1,D:4):1,E:4):1,F:6):1,G:6):1,H:8);
tree rake = (A:1,B:1,C:1,D:1,E:1,F:1,G:1,H:1);
tree rake-cladogram = (A,B,C,D,E,F,G,H);

NEXUS files of dna or protein data with a taxa block

TAXA, CHARACTERS, TREES. May contain an ASSUMPTIONS block with character weigths.

read	plot	Test	Description
pass	pass	SPAN_Family1nlw	SPAN export file, family 1, nucleotides, weights in ASSUMPTIONS block. Internal node labels.
pass	pass	SPAN_Family2alw	SPAN export file, family 2, amino acids, weights in ASSUMPTIONS block. Internal node labels.
pass	pass	SPAN_Family4nl	SPAN export file, family 4, nucleotides. Internal node labels.
pass	pass	SPAN_Family5alw	SPAN export file, family 5, amino acids, weights in ASSUMPTIONS block. Internal node labels.
pass	pass	SPAN_Family7n	SPAN export file, family 7, nucleotides. Internal node labels.
pass	pass	SPAN_Family8a	SPAN export file, family 8, amino acids. Internal node labels.
pass	pass	FaresWolfeCCT	CCT chaperonin amino acids, tree; normalized by nextool; data from Mario Fares (Fares & Wolfe, 2003, Mol Biol Evol. 20: 1588-97)

NEXUS files of dna or protein data with NO taxa block

OTUs are defined implicitly in the data block instead.

read	plot	Test	Description
fail?	ND	UnaSmithHIV-both	HIV sequences. fusion of NEXUS data and trees blocks from separate files supplied by Una Smith. No branch lengths.
fail	ND	barns-combined	fusion of two files from Chuck Delwiche. No TAXA block; tree & data from separate files, names may not match
pass	pass	Bird_Ovomucoids	MacClade example file. No TAXA block. Trees without branch lengths.
pass	pass	Human_mt_DNA	MacClade example file. No TAXA block. Large data set. Trees without branch lengths. Multiple trees.
pass	pass	Kingdoms_DNA	MacClade example file. No TAXA block. Trees without branch lengths.
pass	pass	Marsupial_Wolf	MacClade example file. No TAXA block. Trees without branch lengths.
pass	pass	Primate_mtDNA	MacClade example file. No TAXA block. Trees without branch lengths. Multiple trees.
fail	ND	Omland-Orioles	nucleotide data from Kevin Omland. No TAXA, no TREES blocks. Nucleotides are written in sets of three, with spaces between each codon. Names may not match within data block.
fail	ND	Omland-Ravens	nucleotide data from Kevin Omland. No TAXA, no TREES blocks. Nucleotides are written in sets of three, with spaces between each codon.
pass	pass	Treebase-liverwort-rbcl	Treebase export. rbcL sequence data with tree from analysis of liverwort phylogeny by Lewis, et al., 1997. No TAXA block. No branch lengths.
pass	pass	Treebase-horsetails-dna	dna sequence data with tree. No TAXA block. No branch lengths.
pass	pass	Treebase-chlamy-dna	dna sequence data with tree. No TAXA block. No branch lengths.

NEXUS files of non-dna non-protein data with a taxa block

read	plot	Test	Description
pass	pass	SPAN_Family3il	SPAN export file, family 1, intron presence/absence data. Internal node labels.
pass	pass	SPAN_Family6iw	SPAN export file, family 6, intron presence/absence data, weights in ASSUMPTIONS block. Internal node labels.
pass	pass	SPAN_Family9iw	SPAN export file, family 9, intron presence/absence data, weights in ASSUMPTIONS block. Internal node labels.
pass	pass	SPAN_Family10i	SPAN export file, family 10, intron presence/absence data. Internal node labels.

NEXUS files of non-dna non-protein data with NO taxa block

OTUs are defined implicitly in the data block instead

read	plot	Test	Description
fail	ND	Treebase-horsetails-classic	classic character data with tree. No TAXA block. No branch lengths.

NEXUS errors: non-conformant files with common errors

this section not done, to include common errors:

ntax does not match taxa
nchar does not match chars
names do not match between blocks

Data input (format conversion): alignments and trees in other formats

Sets of alignments with matching trees to be converted and plotted. In practice, both the tree and the alignment are converted to separate NEXUS files, which can be plotted by nexplot, so that we can test four steps: convert alignment or tree; plot alignment or tree; merge alignment and tree into one file; plot alignment with tree.

convert	plot	merge	plot	Test	Description
ND	ND	ND	ND	CuZnSOD.aln	Cu-Zn SOD amino acid sequence alignment (ClustalW output)
ND	ND	ND	ND	CuZnSOD.dnd	ClustalW guide tree (ClustalW output)
ND	ND	ND	ND	TPI.aln	TPI amino acid sequence alignment (ClustalW output)
ND	ND	ND	ND	TPI.dnd	ClustalW guide tree (ClustalW output)
ND	ND	ND	ND	MnFeSOD-rename.phy	Mn-Fe SOD amino acid sequence alignment (ClustalW output). Names were simplified prior to running clustalw to avoid problems by the limit on name lengths in Phylip files.
ND	ND	ND	ND	MnFeSOD-rename.dnd	ClustalW guide tree (ClustalW output)
(NA)	ND	ND	ND	UnaSmithHIV-data.nex	HIV sequences alignment
(NA)	ND	ND	ND	UnaSmithHIV-tree.nex	tree for HIV sequences, no branch lengths
ND	ND	ND	ND	SSU_Mito_rep.gb	from RDBII; representative mito SSU sequences in GenBank format
ND	ND	ND	ND	SSU_Mito_rep.newick	from RDBII; tree with representative mito SSU sequences; labels in tree have embedded data

Data input: tabular data with tree in adjacency-table format

not done: data in the form of text table, tree in the form of adjacency table (e.g., like microarray data)