Man pages for BKapili/ppit
Phylogenetic Placement for Inferring Taxonomy
| nifH_cutoffs_v2 | Patristic distance and pairwise percent identity rank cutoffs... |
| nifH_example_ps | Phyloseq object containing _nifH_ sequences analyzed in... |
| nifH_example_SEPP_alignment | SEPP output alignment for PPIT tutorial. |
| nifH_reference_alignment_v2 | Reference _nifH_ nucleotide alignment (v.1.2.0) |
| nifH_reference_RAxML_info_v2 | RAxML info file for SEPP placement (v.1.2.0) |
| nifH_reference_taxonomy_v2 | Taxonomic and supplementary information for _nifH_ reference... |
| nifH_reference_tree_v2 | Reference _nifH_ gene tree (v.1.2.0) |
| patristic.distance | Calculate patristic distances between query and reference... |
| percent.identity | Calculate pairwise percent identity. |
| ppit | Infer host identities of query sequences. |
| tree.partition | Determine optimal phylogenetic neighborhood threshold. |
