Computational protocol: Streptacidiphilus durhamensis sp. nov., isolated from a spruce forest soil

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Protocol publication

[…] Extraction of genomic DNA, PCR-mediated amplification of the 16S rRNA genes of the three isolates and direct sequencing of the purified PCR products were carried out as described by Golinska et al. (). The search for the closest phylogenetic neighbours based on 16S rRNA gene similarly was performed using the EzTaxon server (http://eztaxon-e.ezbiocloud.net/, Kim et al. ). Phylogenetic analyses were carried out using MEGA 5 (Tamura et al. ) and PHYML (Guindon and Gascuel ) software packages following multiple alignment using Clustal W. Evolutionary distances were calculated and clustering determined using the maximum-likelihood, maximum-parsimony and neighbour-joining methods to generate phylogenetic trees. The topologies of the evolutionary trees were evaluated by a bootstrap analysis (Felsenstein ) derived from 1,000 resamplings of the neighbour-joining dataset using MEGA 5 software. The tree was rooted using the 16S rRNA gene sequence of Streptomyces albus subsp. albus DSM 40313T (GenBank accession number AJ621602). […]

Pipeline specifications

Software tools MEGA, PhyML, Clustal W
Databases EzBioCloud
Application Phylogenetics
Organisms Scaphirhynchus albus