Several of the test files have illegal elements, which are documented in the following table. This list allows parsers to check their error-handling capabilities. This list is not exclusive because not all files have been checked. Page numbers are from the NEXUS standard, Maddison, Swofford and Maddison (1997).
| filename |
caveats
|
| barns-combined
|
- double-quote is not a valid gap symbol (p. 599)
- datatype must be first in format command (p. 599)
|
| char-interleave
|
- datatype must be first in format command (p. 599)
|
| Omland-Ravens
|
- taxon names not identical across interleave pages (p. 603)
|
| quoted-strings1
|
- single (not double) quotes should be used to define tokens with embedded spaces; double-quoted tokens used in taxlabel, charlabel, matrix and tree commands (p. 621)
|
| SPAN_Family3i
|
- the 1 at the end of the tree definition is not allowed because it refers to the first taxon, which has already been included in the tree definition (p. 614)
|
| SPAN_Family4nl
|
- the 1 at the end of the tree definition is not allowed because it refers to the first taxon, which has already been included in the tree definition (p. 614)
- hyphen not allowed inside charstate labels without single-quoting (p. 621)
|
| SPAN_Family6iw
|
- hyphen not allowed inside charstate labels without single-quoting (p. 621)
|
| SPAN_Family7n
|
- the 1 at the end of the tree definition is not allowed because it refers to the first taxon, which has already been included in the tree definition (p. 614)
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| SPAN_Family8a
|
- the 1 at the end of the tree definition is not allowed because it refers to the first taxon, which has already been included in the tree definition (p. 614)
|
| SPAN_Family9iw
|
- hyphen not allowed inside charstate labels without single-quoting (p. 621)
|
| SPAN_Family10i
|
- hyphen not allowed inside charstate labels without single-quoting (p. 621)
|
| trees-translate
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-basal-trifurcation
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-branchlength-negative
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-branchlength-scientific
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-branchlength-zero
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-cladogram
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-extended-root-branch
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-inode-labels-partial
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-inode-labels-quoted1
|
- single quotes should be used to wrap internal node labels in tree description (p. 621)
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-inode-labels-quoted2
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-inode-labels
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-bush-quoted-string-name1
|
- single-quoting should be used to wrap tree name with embedded spaces (p. 621)
|
| trees-tree-bush-uneven
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-ladder-cladogram
|
- O, U and X are not valid state symbols for datatype protein (p. 620)
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-ladder-uneven
|
- O, U and X are not valid state symbols for datatype protein (p. 620)
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-ladder
|
- O, U and X are not valid state symbols for datatype protein (p. 620)
|
| trees-tree-multiple-challenges
|
- should use single quotes for wrapping tree names and internal node names
- O, U and X are not valid state symbols for datatype protein (p. 620)
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| trees-tree-multiple
|
- O, U and X are not valid state symbols for datatype protein (p. 620)
|
| trees-tree-rake-cladogram
|
- hyphen not allowed in tree name without single-quoting (p. 621)
|
| UnaSmithHIV-both
|
- taxon label 'A1.UG.-.UG029' used for two different taxa (p. 598)
|
