List of errors and corrections for NEXUS test set

The definitive version of this file 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 for your local distribution is in the file named VERSION.

NEXUS files with imaginary character data and a taxa block

Test	Title	Description of error
Read	quoted-strings1	ERROR: Number of taxa specified does not equal number of taxa listed: actual number 2 vs dimensions 8.
Read	quoted-strings1	ERROR: Number of taxa specified does not equal number of taxa listed: actual number 2 vs dimensions 8.
Read	top-level-comment	Can't locate object method "write" via package "this file has a top-level comment" (perhaps you forgot to load "this file has a top-level comment"?) at /home/arlin/SPAN/perl/lib/Nexus.pm line 588, line 26.
Read	trees-tree-bush-branchlength-scientific	The tree is not processed correctly, but since the nexus->same does not detect a difference when the tree is written and re-read. The output is: tree bush-branchlength-scientific = (((A:1,Be+01:2)3:1,(Ce-01:9,D:1)4:1)2:1,((E:1,FE-01:9)6:1,(GE+01:2,H:1)7:1)5:1)1;
Read	trees-tree-bush-inode-labels-quoted1	The tree is parsed but 1. labels not dequoted (label text is stored with quotes on it; can tell this from how nexplot behaves). 2. the spaces are removed (e.g., "inodeAB" should be "inode AB": tree bush-inode-labels-quoted1 = (((A:1,B:1)"inodeAB":1,(C:1,D:1)"inodeCD":1)"inodeABCD":1,((E:1,F:1) . . . [stuff deleted]
Read	trees-tree-bush-inode-labels-quoted2	The tree is parsed but the spaces are removed from the inode labels (e.g., 'inodeAB' should be 'inode AB': tree bush-inode-labels-quoted2 = (((A:1,B:1)'inodeAB':1,(C:1,D:1)'inodeCD':1)'inodeABCD':1,((E:1,F:1). . . [stuff deleted]
Read	trees-tree-bush-extended-root-branch	the tree seems to be correct: tree bush-extended-root-branch = (((A:1,B:1)3:1,(C:1,D:1)4:1)2:1,((E:1,F:1)6:1,(G:1,H:1)7:1)5:1)1:1;
Read	trees-tree-multiple-challenges	exhibits "unitialized value" warning, presumably due to cladograms (see cladogram warnings)

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):1,(G:1,H:1):1):1,I:3);
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 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 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.

No problems here.

NEXUS files of dna or protein data with NO taxa block

OTUs are defined implicitly in the data block instead.

Test	Title	Description of error
Read	UnaSmithHIV-both	ND
Read	barns-combined	ND
Read	Bird_Ovomucoids	ND
Read	Human_mt_DNA	ND
Read	Kingdoms_DNA	ND
Read	Marsupial_Wolf	ND
Read	Primate_mtDNA	ND
Read	Omland-Orioles	ND
Read	Omland-Ravens	ND
Read	Treebase-liverwort-rbcl	ND
Read	Treebase-horsetails-dna	ND
Read	Treebase-chlamy-dna	ND

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

Output from SPAN, intron data in TAXA, CHARACTERS, TREES blocks, some with ASSUMPTIONS block.

No problems here.

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

OTUs are defined implicitly in the data block instead

Test	Title	Description of error
Read	Treebase-horsetails-classic	ND

NEXUS errors: non-conformant files with common clerical 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

Alignment files with associated Newick trees

These files are to be converted to a single NEXUS file with alignment and tree. Some are already in NEXUS format and some are not.

Test	Title	Description of error
Read	UnaSmithHIV-data.nex	ND
Read	UnaSmithHIV-tree.nex	ND
Read	SSU_Mito_rep.gb	ND
Read	SSU_Mito_rep.newick	ND

Data tables with adjacency tables

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