Computational protocol: Nitrogen fixation in distinct microbial niches within a chemoautotrophy-driven cave ecosystem

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Protocol publication

[…] For phylogenetic analysis of nifH homologs, we constructed a complete database of cultured representatives of all the standard nifH lineages (), using the ARB software suite (http://www.arb-home.de). The translated amino-acid sequences derived from the sequences obtained in this study were subjected to BLASTp, and the closest nifH sequences (originating from both cultured and uncultured bacteria) were imported in the database. Phylogenetic tree was calculated from the translated amino-acid sequences using the maximum-likelihood algorithm provided in ARB (PhyML with Dayhoff PAM, 100 bootstraps); tree topology was validated with maximum-parsimony analysis (PHYLIP Protein parsimony; 1000 bootstraps). […]

Pipeline specifications

Software tools ARB, BLASTP, PhyML, PHYLIP
Application Phylogenetics
Chemicals Acetylene, Carbon, Nitrogen, Oxygen, Sulfur