References
- Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Computational Biol. 19:455–477.
- Bi G, Mao Y, Xing Q, Cao M. 2018. HomBlocks: a multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching. Genomics. 110:18–22.
- Hahn C, Bachmann L, Chevreux B. 2013. Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads-a baiting and iterative mapping approach. Nucleic Acids Res. 41:e129.
- 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.
- Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32:268–274.
- Okonechnikov K, Golosova O, Fursov M, the UGENE team. 2012. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 28:1166–1167.
- Ruby JG, Priya B, Joseph LD. 2013. PRICE: software for the targeted assembly of components of (Meta) genomic sequence data. G3: Genes, Genomes, Genetics. 3:865–880.
- Wick RR, Schultz MB, Schultz J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 31:3350–3352.