This page will reflect the standard bioinformatics software that is available on the Valhalla system. Valhalla uses the lmod module system to load individual modules for native software packages. Some software packages that require an extensive environment will be made available as apptainer containers.
it is also possible to use containers from container repositories, however we recommend to consult this list first.

Some common workflows are explained in the [analysis guides](https://platecarpus.wur.nl/mibwiki/howtos/running-analyses/).

We try to keep it up to date, for the latest modules you can use the following command:

    module avail

### Bioinformatics tools

| Tool | Version | Load Command | Category | Tags |
|------|---------|-------------|----------|------|
| BLAST | 2.17.0 | `module load ncbi_blast/2.17.0` | Sequence Search & Alignment | `#sequence-search` `#homology` `#database-query` `#functional-annotation` |
| Clustal Omega | 1.2.4 | `module load clustalo/1.2.4` | Multiple Sequence Alignment (MSA) | `#msa` `#phylogenetics` `#conserved-domains` `#protein-alignment` `#dna-alignment` |
| MAFFT | 7.5.2 | `module load mafft/7.525` | Multiple Sequence Alignment (MSA) | `#msa` `#phylogenetics` `#fast-alignment` `#large-datasets` `#protein-alignment` |
| ngtax | 2.2.17 | `module load ngtax/2.2.17` | Amplicon taxonomic classification | `#16S` `#18S` `#amplicon` `#microbiome` `#ASV` `#taxonomic-assignment` `#denoising` `#FAIR` |
| QIIME 2 | 2026.4 | `module load qiime/2026.4` | Microbiome data analysis | `#microbiome` `#diversity-analysis` `#taxonomic-classification` `#alpha-diversity` `#beta-diversity` `#phylogeny` `#amplicon` `#metagenomics` `#provenance` |