Computational protocol: Novel Insights into Regulation of Asparagine Synthetase in Conifers

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Protocol publication

[…] Amino acid sequences deduced from the AS genes of gymnosperms and angiosperms were identified in the GenBank and Phytozome databases, respectively; these sequences were aligned using TCoffee software (Notredame et al., ). The resulting alignment was used to construct a maximum-likelihood phylogenetic tree with a JTT matrix model in Seaview 4.2 software (Gouy et al., ). The statistical support of branches was assessed by approximate likelihood-ratio test (aLRT), which is an alternative to non-parametric bootstrap estimation (Anisimova and Gascuel, ). Jalview 2 software (Waterhouse et al., ) was used to edit the alignment. […]

Pipeline specifications

Software tools T-Coffee, SeaView, Jalview
Databases Phytozome
Application Phylogenetics
Organisms Pinus taeda
Chemicals Adenosine Triphosphate, Nitrogen