Computational protocol: Functional Characterization of Duplicated SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1-Like Genes in Petunia

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Protocol publication

[…] SOC1-like gene sequences of representative angiosperms were downloaded from Genbank after a BLAST search with SOC1 from A. thaliana. The closest A. thaliana SOC1 paralogs AGL14, AGL19, AGL42, AGL72, and AGL71 were also downloaded for reference and to root the tree. Amino acid sequences were aligned manually in Mesquite version 2.75 (). Nucleotide sequences were then subjected to maximum likelihood phylogenetic analysis in GARLI under a GTR+I+Γ model of evolution with 200 bootstrap replicates . […]

Pipeline specifications

Software tools Mesquite, GARLI
Application Phylogenetics
Organisms Arabidopsis thaliana