Computational protocol: Long-Term Effects of Irrigation with Waste Water on Soil AM Fungi Diversity and Microbial Activities: The Implications for Agro-Ecosystem Resilience

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Protocol publication

[…] Phylogenetic analysis was carried out on the sequences obtained in this study and those corresponding to the closest matches from GenBank. Sequences were aligned with other published glomeralean sequences using the program BioEdit software . Neighbour-joining (NJ) and maximum likelihood (ML) phylogenetic analyses were performed with the programs MEGA software v. 4 and RAxML v.7.0.4 , respectively. Distances for the NJ tree were computed using the default parameters. For the ML analysis, a GTR-GAMMA model of evolution was used.Different AMF sequence types or phylotypes, were defined as groups of closely related sequences, usually with a high level of bootstrap support in the phylogenetic analyses (higher than 85%) and sequence similarity ≥ 97%. The pairwise analysis within clusters was carried out using BioEdit software . […]

Pipeline specifications

Software tools BioEdit, MEGA, RAxML
Application Phylogenetics