Computational protocol: Diverse fungi associated with partial irregular heartwood of Dalbergia odorifera

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Protocol publication

[…] The phylogenetic analysis of sequences was based on BLASTn searches of ITS sequence data in the GenBank database. A species was assigned when the identity between the experimental sequences and one in the database was greater than 99%, and the genus was assigned only when matches showed at least 95% identity. When the identity was less than 95%, the strain was considered unidentified. The determined ITS sequences were aligned to other sequences gained from the GenBank database with Clustal X 1.83, and then checked manually. Phylogenetic analysis was performed with MEGA 4.0 using Kimura 2-parameter model with a transition to transversion ration to construct Neighbour-joining (NJ) trees. […]

Pipeline specifications

Software tools BLASTN, Clustal W, MEGA
Application Phylogenetics
Diseases Leukemia, T-Cell