Table 1 NEXUS blocks and common commands
From: Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data
Block name | Commonly used commands | Typical content of block |
|---|---|---|
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 |
DATA 1 | (see CHARACTERS) | OTU labels and character data (deprecated) |