References
- Aguilar A, Truong BR, Gutierrez F. 2018. Complete mitochondrial DNA genomes for two northeast Pacific mesopelagic fishes, the Mexican lampfish (Triphoturus mexicanus) and black-belly dragonfish (Stomias atriventer). Mitochondrial DNA B Resour. 3:21–23.
- Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov AS, Lesin V, Nikolenko S, Pham S, Prjibelski A, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19:455–477.
- Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540–552.
- Iwasaki W, Fukunaga T, Isagozawa R, Yamada K, Maeda Y, Satoh TP, Sado T, Mabuchi K, Takeshima H, Miya M, et al. 2013. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol Biol Evol. 30:2531–2540.
- Joshi NA, Fass JN. 2011. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. https://github.com/najoshi/sickle.
- Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780.
- Kenaley CP. 2012. Exploring feeding behaviour in deep-sea dragonfishes (Teleostei: Stomiidae): jaw biomechanics and functional significance of a loosejaw. Biol J Linn Soc. 106:224–240.
- Kenaley CP, DeVaney SC, Fjeran TT. 2014. The complex evolutionary history of seeing red: molecular phylogeny and the evolution of an adaptive visual system in deep-sea dragonfishes (Stomiiformes: Stomiidae). Evolution. 68:996–1013.
- Miya M, Kawaguchi A, Nishida M. 2001. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol Biol Evol. 18:1993–2009.
- Satoh TP, Miya M, Mabuchi K, Nishida M. 2016. Structure and variation of the mitochondrial genome of fishes. BMC Genomics. 17:719.
- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688–2690.