[maker-devel] RepeatMasker Species Option

[Carson Holt]

RepeatMasker uses NCBI phylogenetic names and other common names.  You can use specific organism names like 'Homo sapiens', or group names like 'mammals', 'vertebrates', or 'chordata'.  There are actually over 5,000 accepted terms.  Try using 'fungi' as your species name.  That should gather together all repeats from all fungal genomes in RepBase into the search space.

Carson

On 10/22/09 4:35 PM, "Daniel Standage" <byuhobbes at gmail.com> wrote:

I spent a bit of time today trying to find an exhaustive list of species options for RepeatMasker, but after re-reading the help statement, it looks like the species options available to you depend on your repeat database. Does this mean I have to scrape the database files to see what species are included? Any suggestions about how to get a list of available species options?  FYI, we want to run maker with a fungal genome.

Thanks!

Daniel Standage
Plant Genetics Lab
Brigham Young University

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