Exclude subspecies?

[Milton Tan]

Is there a good way to handle subspecies? I'm finding that I'm having basically a lot of duplication where there are subspecies, because I get the subspecies AND the species they belong to. I'm curious if there's a way to exclude all the subspecies? Or possibly the reverse, exclude all the species that have subspecies?

[Matthew Nelsen]

Hey Milton,

Can you just add a subspecies term (or set of terms) to your excludes file?  Kind of like how it is done here to get rid of varieties, forms and hybrids?

http://phlawd.net/manual/run-options

-Matt

On Mon, Mar 2, 2015 at 8:10 AM, Milton Tan <mtyou...@gmail.com> wrote:

Is there a good way to handle subspecies? I'm finding that I'm having basically a lot of duplication where there are subspecies, because I get the subspecies AND the species they belong to. I'm curious if there's a way to exclude all the subspecies? Or possibly the reverse, exclude all the species that have subspecies?

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[Milton Tan]

Subspecies don't have anything consistent about them that can be excluded from the search term, as far as I know, except that they have three names instead of two. Perhaps there's something with that to put in the exclude file but I'm not sure what exactly I'd put.

I got around this by using grep to exclude taxa that contain two underscores in the final alignment, but I imagine it'd be more efficient to exclude them before alignment.