References
- Beck N, Lang BF. 2010. MFannot, organelle genome annotation webserver. http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl.
- Boetzer M, Pirovano W. 2014. SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information. BMC Bioinf. 15:211.
- Guy L, Kultima JR, Andersson SGE. 2010. genoPlotR: comparative gene and genome visualization in R. Bioinformatics. 26:2334–2335.
- Katoh K, Standley DM. 2013. MAFFT Multiple Sequence Alignment Software Version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780.
- Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964.
- Song JH, Kim S, Shin S, Min GS. 2016. The complete mitochondrial genome of the mysid shrimp, Neomysis japonica (Crustacea, Malacostraca, Mysida). Mitochondrial DNA A DNA Mapp Seq Anal. 27:2781–2782.
- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688–2690.
- Swart EC, Nowacki M, Shum J, Stiles H, Higgins BP, Doak TG, Schotanus K, Magrini VJ, Minx P, Mardis ER, Landweber LF. 2011. The Oxytricha trifallax mitochondrial genome. Genome Biol Evol. 4:136–154.
- Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564–577.