Ecology and phylogeny of nitric oxide producing nitrite reductases NirK and NirS

nirK_2021_woutgroup.faa.fasta: Amino acid alignment of Cu-type nitrite reductase proteins and outgroupNirK_export_from_ITOL_bootstraps.nwk: Maximum likelihood tree of amino acid alignment of Cu-type nitrite reductase proteins and outgroupNirS_2021_alignment.fasta: Amino acid alignment of cytochrome cd1-type nitrite reductase proteins and outgroupsNirS_export_from_ITOL_bootstraps.nwk: Maximum likelihood tree of amino acid alignment of cytochrome cd1-type nitrite reductase proteins and outgroupsGToTree_HugGenes_NirKS.nwk.treefile: "organism" phylogeny of assemblies used in NirK and NirS reference phylogenies, using genes searched by GToTree for the "Hug et al" single copy gene setNirK_2021.gpkg: reference package for GraftM search of NirK in metagenomesnirS_2021_refpack.gpkg: reference package for GraftM search of NirS in metagenomesclade_specific_HMMs: folder containing fasta amino acid sequences and HMMs for each clade in the NirK and NirS reference trees. Models are provided as-is. Users must validate the appropriate e-value cutoffs to optimize sensitivity and specificity for their own purposes.Additional interactive versions of trees can be found in ITOL under: https://itol.embl.de/tree/772352422250261699024512# and https://itol.embl.de/tree/77235243231271051662352824