Table IV. Locations of all software and data sets
Software, User Tutorials, or Data SetsDownload Location and Password if Applicable
MAKER-P (version 2.29) downloadhttp://www.yandell-lab.org/software/maker-p.html
WebApollo downloadhttps://code.google.com/p/apollo-web/downloads/list
TAIR10, maize, and MAKER-P annotation GFF3 fileshttp://weatherby.genetics.utah.edu/A_thaliana/ (username, MAKER-P; password, marksentme)
iPlant MAKER-P documentationhttps://pods.iplantcollaborative.org/wiki/display/sciplant/MAKER-P+Documentation
Basic MAKER tutorialhttp://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial
Pseudogene pipeline download and tutorialhttp://shiulab.plantbiology.msu.edu/wiki/index.php/Protocol:Pseudogene
miR-PREFeRhttps://github.com/hangelwen/miR-PREFeR
tRNAscan-SEhttp://selab.janelia.org/software.html
snoscanhttp://lowelab.ucsc.edu/snoscan/
Basic repeat library construction tutorialhttp://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Basic
Advanced repeat library construction tutorialhttp://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced