Computational protocol: Diversity and Biosynthetic Potential of Culturable Microbes Associated with Toxic Marine Animals

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Protocol publication

[…] Partial sequences of 16S rRNA genes obtained from this study, as well as 42 reference sequences obtained from NCBI Genbank, were aligned using Muscle []. A phylogenetic tree was constructed from a 539 bp alignment with maximum likelihood algorithm, PhyML [], using the general time reversible with gamma distribution (GTR + G) base substitution model determined using the web-based application, FindModel []. The tree was rooted with Synechocystis sp. PCC 6803 (Genbank accession number AY224195.1) as an outgroup. The aLRT SH-like approach was used as an estimate of branch reliability []. […]

Pipeline specifications

Software tools MUSCLE, PhyML
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Pomacea maculata
Chemicals Tetrodotoxin