search

naturalis / supersmart

Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
MIT License
17 stars 5 forks source link

User can specify lowest taxonomic level to be included in trees #16

Closed alexantonelli closed 10 years ago

alexantonelli commented 10 years ago

The default should be that only one species per genus is included in the second analytical step (the species-level analysis). This will enable further spatial analyses, which often will use the species total geographic range in biogeography. The big assumption here is that species are always monophyletic (which is not always true but needed for spatial analyses).

As an alternative, the user could specify that supersmart downloads data for all taxonomic levels, including below the species level: e.g. subspecies, varieties, and different individuals. This option will be preferred for those mostly interested in phylogenetic relationships and divergence times.

hettling commented 10 years ago

From revision 8c24f99adda84b0088fe2cfc50957ed5dacd07d6, the user can specify the lowest taxonomic rank in the variable LOWEST_TAXON_RANK in phylota.ini. If the variable has no value, all taxonomic ranks are possible.

rvosa commented 10 years ago

I think this option is now resolved, so let's close it.