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NEXUS blocks and common commands |
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| Block name |
Commonly used commands |
Typical content of block |
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| TAXA |
dimensions, taxlabels |
Labels for OTUs (may be quoted strings) |
| CHARACTERS |
dimensions, format, matrix |
A matrix of character-state data (e.g., aligned residues) of defined type, in a defined format |
| TREES |
tree, translate |
Rooted or unrooted trees in Newick format, with optional names and weights for each tree |
| ASSUMPTIONS |
options, usertype, wtset |
Constraints on allowed changes; transition cost model; weights for characters |
| CODONS |
codonposset, geneticcode |
Description of a reading frame and the genetic code used to translate it |
| SETS |
charset, taxset, treeset |
Named sets of OTUs (taxsets), trees, characters, states, or state transitions (changesets) |
| NOTES |
text, picture |
Annotations attaching text or pictures to sets of objects including OTUs, characters or trees |
| DISTANCES |
dimensions, format, matrix |
Distance matrices |
| UNALIGNED |
dimensions, format, matrix |
Unaligned data |
| DATA1 |
(see CHARACTERS) |
OTU labels and character data (deprecated) |
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1 The DATA block format, though commonly used, is deprecated so as to encourage use of a separately declared list of OTUs in a TAXA block. | ||
Hladish et al. BMC Bioinformatics 2007 8:191 doi:10.1186/1471-2105-8-191 |
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