Computational protocol: Phylogenomic Investigation of Phospholipid Synthesis in Archaea

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Protocol publication

[…] Sequence seeds for similarity searches were retrieved from the KEGG database ( Searches were carried out with BLASTp [] against a list of completely sequenced genomes available in GenBank (Supplementary Table 1). The resulting sequences were aligned with by default parameters with Muscle 3.6 []. Redundant and partial sequences were removed and ambiguously aligned regions were discarded prior to phylogenetic analyses using the NET program from the MUST package []. Phylogenetic trees were reconstructed with the approximately maximum likelihood approach with FastTree 2.1.3 []. […]

Pipeline specifications

Software tools BLASTP, MUSCLE, FastTree
Databases KEGG
Applications Phylogenetics, Nucleotide sequence alignment
Chemicals Ether, Fatty Acids, Terpenes