##Seqnature is replaced!
The Jackson Laboratory has released a new tool, g2gtools, with a superset of the features in the seqnature suite. Please use it instead.
Seqnature is no longer in maintenance.
The g2gtools are available at: https://github.com/churchill-lab/g2gtools.
If you use Seqnature for your published research, please cite:
Munger SC, Raghupathy N, Choi KB, Simons AK, Gatti DM, Hinerfeld DA, Svenson KL, Keller MP, Attie AD, Hibbs MA, Graber JH, Chesler EJ, and Churchill GA. RNA-seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations. GENETICS, In Press.