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

<b>nirK_2021_woutgroup.faa.fasta: </b>Amino acid alignment of Cu-type nitrite reductase proteins and outgroup<b>NirK_export_from_ITOL_bootstraps.nwk:</b> Maximum likelihood tree of amino acid alignment of Cu-type nitrite reductase proteins and outgroup<b>NirS_2021_alignment.fasta: </b>Amino acid alignment of cytochrome cd1-type nitrite reductase proteins and outgroups<b>NirS_export_from_ITOL_bootstraps.nwk:</b> Maximum likelihood tree of amino acid alignment of cytochrome cd1-type nitrite reductase proteins and outgroups<b>GToTree_HugGenes_NirKS.nwk.treefile:</b> "organism" phylogeny of assemblies used in NirK and NirS reference phylogenies, using genes searched by GToTree for the "Hug et al" single copy gene set<b>NirK_2021.gpkg:</b> reference package for GraftM search of NirK in metagenomes<b>nirS_2021_refpack.gpkg:</b> reference package for GraftM search of NirS in metagenomes<b>clade_specific_HMMs:</b> 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<br>