One can easily work with species functional traits or import the data on phylogenetic relatedness of species.
The above snapshot of the Canoco 5 workspace displays (in the background) a data notebook with multiple data tables. The Species data table contains information about community composition, while the currently visible Traits table shows the known traits for individual species. You can also calculate, for individual cases, the averages of individual traits (implemented also for factorial traits) and analyse such table directly. Further, when doing analyses for individual community species acting as cases, it might be appropriate to perform phylogenetic correction during the tests. Canoco 5 supports this in the form of the Desdevises method and for this it allows importing a phylogenetic tree in Newick format and transforming it into a matrix of patristic distances, as illustrated by the dialog box in the front of the snapshot. In Canoco 5 you can also easily make nice biplots of RLQ analyses with traits and environmental variables.