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Sequence data were aligned and analyzed using the MEGA package.
Phylogenetic analyses and statistical neighbour-joining bootstrap tests of the phylogenies were carried out using the Mega package [26].
The unrooted tree was drawn using the MEGA package [ 86].
The alignment quality was improved by manually editing the MSA using the MEGA package.
Phylogenetic trees will be constructed using the MEGA package [ 41], and a bootstrap analysis [ 42] will be performed.
The phylogenetic analysis of genotypes of the rat strains was performed using the MEGA package [ 19] and Splitstree [ 20].
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The sequences of this small section were selected, realigned with CLUSTALX, and Neighbor-joining trees based on the distance parameter were constructed using the MEGA 4 package.
Duplicates and incomplete proteins were removed, and multiple alignments were constructed with the CLUSTALX program [60] and an initial phylogenetic tree was created using the MEGA 4 package.
The maximum parsimony and neighbor-joining trees were obtained using the MEGA 5 package [ 61].
Phylogenetic analyses was carried out using the MEGA 4 package [ 46] with neighbour-joining bootstrap tests (1000 times).
A phylogenetic tree was constructed using maximum-likelihood (ML) algorithms based on the K2+G+I model with 1000 bootstrap replications using the MEGA 5.2.2 package.
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