The complete mitochondrial transcript of the red tail loach Yasuhikotakia modesta as assembled from RNAseq (Teleostei: Botiidae)

Figures & data

Figure 1. Maximum-likelihood tree illustrating the phylogenetic position of the newly sequenced Y. modesta gene sequence among a subset of Botiidae species. Cytochrome B sequences were aligned using MAFFT 7.271 and highly divergent or poorly aligned regions were removed with Gblocks 0.91b (Castresana 2000) allowing for gap positions and smaller blocks. Trees were calculated using PhyML 3.1 (Guindon et al. 2010) with 12 rate categories, optimized equilibrium frequencies, GTR model of sequence evolution and combined heuristics (nearest neighbour interchange and subtree pruning and rerafting).

Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540–552.

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Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 59:307–321.

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