Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Software, algorithm | Snakemake | Snakemake | RRID: SCR_003475 | Workflow manager |
| Software, algorithm | Prodigal | Prodigal | RRID: SCR_021246 | Gene prediction |
| Software, algorithm | MMseqs2 | MMseqs2 | RRID: SCR_010277 | Sequence clustering and search |
| Software, algorithm | HHMER | HMMER | RRID: SCR_005305 | Sequence-Profile search |
| Software, algorithm | HHblits | HHblits | RRID: SCR_010277 | Profile-Profile search |
| Software, algorithm | PARASAIL | PARASAIL | RRID:SCR_021805 | Sequence alignment |
| Software, algorithm | FAMSA | FAMSA | RRID:SCR_021804 | Sequence alignment |
| Software, algorithm | LEON-BIS | LEON-BIS | RRID:SCR_021803 | Sequence alignment evaluation |
| Software, algorithm | OD-SEQ | OD-SEQ | Sequence alignment http://www.bioinf.ucd.ie/download/od-seq.tar.gz | |
| Software, algorithm | SEQKIT | SEQKIT | RRID: SCR_018926 | Fasta file manipulation |
| Software, algorithm | R | R | RRID: SCR_002394 | |
| Software, algorithm | HH-SUITE | HH-SUITE | RRID: SCR_016133 | |
| Software, algorithm | RAXML | RAXML | RRID: SCR_006086 | Phylogeny |
| Software, algorithm | PPLACER | PPLACER | RRID: SCR_004737 | Phylogeny |
| Software, algorithm | PAPARA | PAPARA | Sequence alignment https://cme.hits.org/exelixis/resource/download/software/papara_nt-2.5-static_x86_64.tar.gz | |
| Software, algorithm | Anvi’o | Anvi’o | RRID:SCR_021802 | Omics analysis and visualization https://merenlab.org/software/anvio |
| Software, algorithm | BWA mapper | BWA mapper | RRID: SCR_010910 | Sequence alignment |
| Software, algorithm | BEDTOOLS | BEDTOOLS | RRID: SCR_006646 | |
| Software, algorithm | PhageBoost | PhageBoost | https://github.com/ku-cbd/PhageBoost | |
| Software, algorithm | EGGNOG-mapper | EGGNOG-mapper | RRID: SCR_021165 |