Table IV. Locations of all software and data sets.

Software, User Tutorials, or Data Sets	Download Location and Password if Applicable
MAKER-P (version 2.29) download	http://www.yandell-lab.org/software/maker-p.html
WebApollo download	https://code.google.com/p/apollo-web/downloads/list
TAIR10, maize, and MAKER-P annotation GFF3 files	http://weatherby.genetics.utah.edu/A_thaliana/ (username, MAKER-P; password, marksentme)
iPlant MAKER-P documentation	https://pods.iplantcollaborative.org/wiki/display/sciplant/MAKER-P+Documentation
Basic MAKER tutorial	http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial
Pseudogene pipeline download and tutorial	http://shiulab.plantbiology.msu.edu/wiki/index.php/Protocol:Pseudogene
miR-PREFeR	https://github.com/hangelwen/miR-PREFeR
tRNAscan-SE	http://selab.janelia.org/software.html
snoscan	http://lowelab.ucsc.edu/snoscan/
Basic repeat library construction tutorial	http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Basic
Advanced repeat library construction tutorial	http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced