Maddison, D.R., Swofford D.L., and Maddison W.P. (1997) NEXUS: An extensible file format for systematic information. Systematic Biology, 46, 590-621.
"p.594: Programs that read NEXUS files do not have to be able to understand all aspects of the file format; In fact, no program at this time can understand more than about 60% of elements described in this document.
object definition command : see page 619 of standards.
| Key words | Blocks | Is Command | Is Obj. Def. | Modifies command | Arguments | # of blocks using command | # in Bio:: NEXUS | Comment |
|---|---|---|---|---|---|---|---|---|
| #NEXUS | - | FALSE | FALSE | - | 1 | 1 | ||
| begin | all | TRUE | FALSE | - | 10 | 10 | ||
| taxa | taxa | FALSE | FALSE | begin | 1 | 1 | ||
| dimensions | "taxa, characters, unaligned, distances" | TRUE | FALSE | - | 4 | 4 | "In taxa block, must appear before taxlabels; in characters block must proceed charlabels, charstatelabels, statelabels, , matrix" | |
| ntax | "taxa, distances" | FALSE | FALSE | "dimensions, newtaxa" | number-of-taxa | 3 | 3 | use only in taxa block or with newtaxa command |
| taxlabels | "taxa, characters, unaligned, distances" | TRUE | FALSE | - | taxon-name .. | 4 | 4 | "taxon names- ""must not correspond to another taxon name or number""" |
| end | all | TRUE | FALSE | 10 | 10 | the synonym "endblock" also is supported | ||
| characters | characters | FALSE | FALSE | begin | 1 | 1 | ||
| newtaxa | "characters, unaligned, distances" | TRUE | FALSE | dimensions | ntax | 3 | 0 | Must appear before ntax. deprecated. |
| nchar | "characters, distances" | FALSE | FALSE | dimensions | number-of-characters | 2 | 2 | |
| format | "characters, unaligned, distances" | TRUE | FALSE | - | 3 | 3 | "in characters block must proceed charlabels, charstatelabels, statelabels, matrix" | |
| datatype | "characters, unaligned" | TRUE | FALSE | format | {standard | DNA | RNA | nucleotide | protein | continous} | 2 | 2 | |
| respectcase | "characters, unaligned" | TRUE | FALSE | format | none | 2 | 0 | |
| missing | "characters, unaligned, distances" | TRUE | FALSE | format | symbol | 3 | 3 | |
| gap | characters | TRUE | FALSE | format | symbol | 1 | 1 | |
| symbols | "characters, unaligned" | TRUE | FALSE | format | "symbol .." | 2 | 2 | |
| equate | "characters, unaligned" | TRUE | FALSE | format | "symbol = entry .." | 2 | 0 | |
| matchchar | characters | TRUE | FALSE | format | symbol | 1 | 0 | |
| labels | "characters, unaligned, distances" | TRUE | FALSE | format | none | 3 | 3 | mutually exclusive with nolabels |
| nolabels | "characters, unaligned, distances" | TRUE | FALSE | format | none | 3 | 3 | mutually exclusive with labels |
| transpose | characters | TRUE | FALSE | format | none | 1 | 0 | |
| interleave | "characters, distances" | TRUE | FALSE | format | none | 2 | 2 | |
| items | characters | TRUE | FALSE | format | (items ..) items = {min | max | median | average | variance | stderror | samplesize | states} | 1 | 1 | no checking of values (makes no sense to do so without dependent methods) |
| statesformat | characters | TRUE | FALSE | format | {statespresent | individuals | count | frequency} | 1 | 1 | |
| tokens | characters | TRUE | FALSE | format | none | 1 | 1 | mutually exclusive with notokens |
| notokens | characters | TRUE | FALSE | format | none | 1 | 1 | mutually exclusive with tokens |
| eliminate | characters | TRUE | FALSE | - | character-set | 1 | 0 | "in characters block must proceed charlabels, charstatelabels, statelabels, matrix" |
| charstatelabels | characters | TRUE | FALSE | - | character-number character-name/ state-name .. | 1 | 1 | |
| charlabels | characters | TRUE | FALSE | - | character-name .. | 1 | 1 | |
| statelabels | characters | TRUE | FALSE | character-number state-name .. | 1 | 1 | ||
| matrix | "characters, unaligned, distances" | TRUE | FALSE | - | data-matrix | 3 | 3 | |
| unaligned | unaligned | FALSE | FALSE | begin | - | 1 | 1 | |
| distances | distances | FALSE | FALSE | begin | - | 1 | 1 | |
| triangle | distances | TRUE | FALSE | format | {lower | upper | both} | 1 | 1 | |
| diagonal | distances | TRUE | FALSE | format | 1 | 1 | mutually exclusive with nodiagonal | |
| nodiagonal | distances | TRUE | FALSE | format | 1 | 1 | mutually exclusive with diagonal | |
| data | data | FALSE | FALSE | begin | 1 | 1 | Equivalent to characters block where the newtaxa subcommand is included in the dimensions command. Deprecated | |
| codons | codons | FALSE | FALSE | begin | - | 1 | 1 | currently, block is read but no commands supported |
| codonposset | codons | TRUE | TRUE | "codonposset [*] name [({standard | vector}) = N: character-set, 1: character-set, 2: character-set, 3: character-set;" | 1 | 0 | ||
| geneticcode | codons | TRUE | TRUE | geneticcode code-name = genetic-code-description | 1 | 0 | "predefined code-names = "universal, universtal.ext, mtdna.dros, mtdna.dros.ext, mtdna.mam, mtdna.mam.ext, mtdna.yeast" | |
| codeorder | codons | TRUE | FALSE | geneticcode | 132 or other | 1 | 0 | |
| nucorder | codons | TRUE | FALSE | geneticcode | TCAG or other | 1 | 0 | |
| tokens | codons | TRUE | FALSE | geneticcode | 1 | 0 | mutually exclusive with notokens | |
| notokens | codons | TRUE | FALSE | geneticcode | 1 | 0 | mutually exclusive with tokens | |
| extensions | codons | TRUE | FALSE | geneticcode | symbol .. | 1 | 0 | |
| codeset | codons | TRUE | TRUE | codeset [*] code-set-name [({characters | unaligned | taxa})] = code-name: character-set or taxon-set .. or all | 1 | 0 | ||
| sets | sets | FALSE | FALSE | begin | 1 | 1 | ||
| charset | sets | TRUE | TRUE | - | charset charset-name [( {standard | vector})] = character-set | 1 | 0 | |
| stateset | sets | TRUE | TRUE | - | stateset stateset-name [({standard | vector})] = state-set | 1 | 0 | |
| changeset | sets | TRUE | TRUE | - | changeset changeset-name = state-set <-> state-set .. | 1 | 0 | |
| taxset | sets | TRUE | TRUE | - | taxset taxset-name [({standard | vector})] = taxon-set | 1 | 1 | |
| treeset | sets | TRUE | TRUE | - | "treeset charset-name [({standard, vector})] = character-set" | 1 | 0 | |
| charpartition | sets | TRUE | TRUE | - | charpartition partition-name [({standard | vector}) {tokens | notokens}] = subset-name : character-set | 1 | 0 | |
| tokens | sets | TRUE | FALSE | "charpartition, taxpartition, treepartition" | none | 1 | 0 | mutually exclusive with notokens |
| notokens | sets | TRUE | FALSE | "charpartition, taxpartition, treepartition" | none | 1 | 0 | mutually exclusive with tokens |
| taxpartition | sets | TRUE | TRUE | - | taxpartition partition-name [({standard | vector}) {tokens | notokens}] = subset-name : taxon -set | 1 | 0 | |
| treepartition | sets | TRUE | TRUE | - | treepartition partition-name [({standard | vector}) {tokens | notokens}] = subset-name : tree-set | 1 | 0 | |
| assumptions | assumptions | FALSE | FALSE | begin | 1 | 1 | ||
| options | assumptions | TRUE | FALSE | - | 1 | 1 | ||
| deftype | assumptions | TRUE | FALSE | options | deftype = type-name | 1 | 1 | |
| polytcount | assumptions | TRUE | FALSE | options | {minstep | maxsteps} | 1 | 1 | |
| gapmode | assumptions | TRUE | FALSE | options | {missing | newstate} | 1 | 1 | |
| usertype | assumptions | TRUE | TRUE | - | usertype type-name [({stepmatrix | cstree})] = usertype-description | 1 | 0 | |
| typeset | assumptions | TRUE | TRUE | - | "typeset [*] typeset-name [(standard, vector)] = type-set-definition" | 1 | 0 | |
| wtset | assumptions | TRUE | TRUE | - | wtset [*] wtset-name [({standard | vector})] = wtset-definition | 1 | 1 | |
| exset | assumptions | TRUE | TRUE | - | exset [*] exset-name [({standard | vector})] = exset-definition | 1 | 0 | |
| ancstates | assumptions | TRUE | TRUE | - | ancstates [*] ancstates-name [({standard | vector})] = ancstates-definition | 1 | 0 | |
| trees | Trees | FALSE | FALSE | begin | 1 | 1 | ||
| translate | Trees | TRUE | FALSE | - | 1 | 1 | ||
| tree | Trees | TRUE | TRUE | tree [*] tree-name = tree-specification | 1 | 1 | ||
| [&R] | Trees | FALSE | FALSE | tree | 1 | 1 | ||
| [&U] | Trees | FALSE | FALSE | tree | 1 | 1 | ||
| notes | notes | FALSE | FALSE | begin | 1 | 1 | currently, block is read but no commands supported | |
| text | notes | TRUE | FALSE | text [ taxon = taxon-set] [character = character-set] [state = state-set][ tree = tree-set] source = {inline | file | resource} text = text-or-source descriptor | 1 | 0 | ||
| picture | notes | TRUE | FALSE | picture [ taxon = taxon-set] [character = character-set] [state = state-set][ tree = tree-set] [format = {PICT | TIFF | EPS | JPEG | GIF}] source = {inline | file | resource} picture = picture-or-source descriptor | 1 | 0 | ||
| taxon | notes | FALSE | FALSE | "text, picture" | 1 | 0 | ||
| character | notes | FALSE | FALSE | "text, picture" | 1 | 0 | ||
| state | notes | FALSE | FALSE | "text, picture" | 1 | 0 | ||
| tree | notes | FALSE | FALSE | "text, picture" | 1 | 0 | ||
| source | notes | FALSE | FALSE | "text, picture" | 1 | 0 | ||
| text | notes | FALSE | FALSE | text | 1 | 0 | ||
| encode | notes | FALSE | FALSE | picture | 1 | 0 | ||
| picture | notes | FALSE | FALSE | picture | 1 | 0 |
(Made by Vivek and Arlin, August 8th 2006)