It has always been a challenge for microbiologists to use Nitogen fixing gene as a marker for inferring microbial taxonomy . Environmental Biologists have been linking ecological functions to the microbial communities, thus, making it possible for them to work out the phylogenies for these microbes. Nitogen fixing gene nif has been used as a marker for many years now and with the sequencing of this gene, it has started being used for inferring taxonomy.
In their recent work, Dekas A.E. et.al.(2021) have developed an R package called Phylogenetic Placement for Inferring taxonomy (PPIT) for building microbial taxonomy using nif gene.They have also discussed the use of this package for other marker genes.The package is freely available at the following website https://github.com/bkapili/ppit.
Reference:
Dekas A.E. et. al. (2021) PPIT: an R package for inferring microbial taxonomy from nifH sequences. Bioinformatics 37(16):2289-2298