Computational protocol: Evolution of hydra, a Recently Evolved Testis-Expressed Gene with Nine Alternative First Exons in Drosophila melanogaster

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Protocol publication

[…] Sequences were aligned using ClustalW [], with some manual adjustment to keep gaps in-frame in coding regions. Phylogenetic analyses were performed using Mega 3.1 []. Sequence polymorphism and divergence analysis were done using DnaSP 4.10 []. The effective number of synonymous and nonsynonymous sites, Ka and Ks values, and pairwise divergence for synonymous sites based on Kimura's two-parameter model were estimated. […]

Pipeline specifications

Software tools Clustal W, MEGA, DnaSP
Application Phylogenetics
Organisms Drosophila melanogaster, Drosophila ananassae, Drosophila pseudoobscura, Drosophila simulans, Drosophila sechellia, Drosophila yakuba