Computational protocol: Nitrogen Fixation in Denitrified Marine Waters

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Protocol publication

[…] A total of 1125 valid sequences were obtained in this study, 437 for the Knorr cruise and 688 for the Galathea expedition (more detailed information is given in , , , and ). Representative clones, one from each of the different phylogenetic groups identified based on ≥95% nucleotide similarity (, , , and ), were used to construct the phylogenetic trees. Sequence alignment in the amino acid space was performed with MUSCLE 3.6 . The maximum-likelihood phylogenetic tree in was constructed with PhyML using the default parameters in the program Bosque . Percentages of Bootstrap support values (≥50) based on 1000 replications are shown at the nodes. Sequence data were deposited in the GenBank database under accession numbers HM801148 to HM801841. […]

Pipeline specifications

Software tools MUSCLE, PhyML, Bosque
Applications Phylogenetics, Nucleotide sequence alignment
Chemicals Ammonia, Nitrogen, Oxygen