Adding basic CQL parser. Parses CQL query into a nested object for conversion to the appropriate SPARQL query.
Adding info about command line help to README.
Adding tree_name parameter to change the name of the tree node.
Figured out how to use SPARQL with named graphs in Redland/Virtuoso. Replacing former kludgy list_trees method with new version.
Pass a list of species to list_trees to get back only trees that contain each of those species.
Minor query warning fix.
Use blank nodes when results aren't needed and use Redland_python to suppress warnings.
Reset callback handler after changing it.
cqlQuery term doesn't need to be recursively defined.
list_trees can now match lists of taxa and can return trees that don't match the entire list; this can be used to find the tree that best fits a query.
Added DendroPy in order to fully support adding of trees in NEXUS files.
Since results are sorted by match quality, list_trees should be a generator.
Treestore.get_names: get a list of names recognized by the treestore.
Alphabetize treestore ls when no list of taxa is given, but order by match score when a list is given.
Get names/uris in CSV, JSON, or XML.
Add tree's base URI to OTU URI to form complete URI.
Fixing graph URI issue.
Removing DISTINCT seems to fix match sorting.
Merge conflict resolution.
Added support for adding N-Triples to a tree. This is used for enhancing a tree with annotations.