Computational protocol: Multiple Episodic Evolution Events in V1R Receptor Genes of East-African Cichlids

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Protocol publication

[…] DNA sequences were edited using GENETYX-Windows version 5. MEGA 5 software () was used to construct neighbor joining trees to estimate the ancestral sequences and to calculate genetic distance and divergence time. The MODELTEST version 3.7 program () was used to determine the model of DNA-sequence evolution that best fit our data sets. To run MODELTEST, PAUP* 4.0b10 () was used. The PHYML program () was used to construct the ML tree based on the MODELTEST model. The haplotype network tree was constructed using TCS (). The π, Tajima’s D values, and degree of linkage disequilibrium (D′) were calculated using DnaSP 5 (). The sequence logo of V1Rs was generated using a web-based program, Weblogo 3.3., available at (last accessed May 1, 2014) (). […]

Pipeline specifications

Software tools MEGA, ModelTest-NG, PhyML, DnaSP, WebLogo
Applications Phylogenetics, Population genetic analysis, Genome data visualization
Organisms Hemisus marmoratus, Martes pennanti