Table 1 |
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PhyloPattern syntax for representing trees and patterns |
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<node> |
::= |
<leaf> | <internal_node> | <rake> |
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<leaf> |
::= |
" [" <empty_list>, <tag_list> "]" |
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<internal_node> |
::= |
" [" "[" <node>, <node> "]", <tag_list> "]" |
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<rake> |
::= |
&(" [" <node_list> "]") |
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<node_list> |
::= |
<node> |
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::= |
<node>, <node_list> |
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<empty_list> |
::= |
"[]" |
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<tag_list> |
::= |
<empty_list> |
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::= |
" [" <filled_tag_list> "]" |
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<filled_tag_list> |
::= |
<tag> |
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::= |
<tag>, <filled_tag_list> |
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<tag> |
::= |
<identifier> (<value>) |
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<leaf_list> |
::= |
<leaf> |
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::= |
<leaf>, <leaf_list> |
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<identifier> |
::= |
<lower-case-letter> { <letter> | <digit>} |
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::= |
' { <character> } ' |
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<value> |
::= |
<identifier> | <number> |
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<pattern> |
::= |
<leaf> |
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::= |
" [" "[" <pattern>, <pattern> "]", <tag_list> "]" |
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::= |
&(" [" <pattern_list> "]") |
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::= |
@ (<pattern>) |
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::= |
$ (<pattern>) |
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::= |
#(" [" <leaf_list> "]") |
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<pattern_list> |
::= |
<pattern> |
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::= |
<pattern>, <pattern_list> |
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The grammar rules used for describing trees and patterns are indicated using the BNF (Bacchus Naur Form: http://cui.unige.ch/db-research/Enseignement/analyseinfo/AboutBNF.html webcite) notation. |
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Gouret et al. BMC Bioinformatics 2009 10:298 doi:10.1186/1471-2105-10-298 |
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