Computational protocol: Cytokinin Metabolism of Pathogenic Fungus Leptosphaeria maculans Involves Isopentenyltransferase, Adenosine Kinase and Cytokinin Oxidase/Dehydrogenase

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Protocol publication

[…] Protein homology searches were performed using BLASTp implemented in NCBI. For L. maculans, queries were compared to JN3 genome (). Protein sequences were aligned with the MUSCLE program as implemented in www.phylogeny.fr (). The Maximum-likelihood phylogenetic tree was generated with SeaView version 4 software () using a LG substitution model and bootstrapping with 100 replications. The tree was displayed with MEGA 5.2.2. software (). […]

Pipeline specifications

Software tools BLASTP, Phylogeny.fr, SeaView, MEGA
Application Phylogenetics
Organisms Leptosphaeria maculans, Brassica napus
Chemicals Adenosine, Nucleotides