Computational protocol: Genetic evidence from mitochondrial DNA corroborates the origin of Tibetan chickens

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Protocol publication

[…] The nucleotide diversity and haplotypes of all sequences were estimated with DnaSP 5.0 []. Network 5.0 software [] was used to draw maximum parsimony median-joining (MP) network plots. All sequences were aligned with CLUSTAL W [] prior to phylogenetic analysis using the Bayesian Evolutionary Analysis by Sampling Trees (BEAST) 1.7 []. The GTR substitution model with the invariant sites and gamma distribution (GTR+I+G) was selected as the best-fitting model using the jModelTest 2.1.1 []. The length of MCMC was set to 30,000,000 and sampled every 1,000 generations with 10% burn-in. The maximum clade credibility tree was created using TreeAnnotator []. DomeTree and MitotoolPy were used to identify mutations and standard haplogroups in each sequences []. […]

Pipeline specifications

Software tools DnaSP, Clustal W, BEAST, jModelTest
Application Phylogenetics
Organisms Gallus gallus, Homo sapiens