csubst dataset

csubst dataset

csubst dataset copies bundled example datasets into the current working directory. Use it to check an installation, reproduce wiki examples, or create a small input set before trying a new workflow.

Minimal command

csubst dataset --name PGK

Available datasets:

• PGK: a compact test dataset used in many basic examples
• PEPC: a larger example with foreground formats useful for advanced tests

What it writes

The command writes dataset files into the current directory. FASTA files are written as gzip-compressed files, for example:

• alignment.fa.gz
• untrimmed_cds.fa.gz
• tree.nwk
• foreground.txt

Some datasets also include additional foreground tables such as foreground.tsv.

Bundled IQ-TREE intermediate files are copied under csubst_iqtree/ by default. Use --iqtree_outdir PATH to place them elsewhere.

Typical next steps

Run input validation:

csubst doctor \
  --alignment_file alignment.fa.gz \
  --rooted_tree_file tree.nwk \
  --foreground foreground.txt

Then run the main search:

csubst search \
  --alignment_file alignment.fa.gz \
  --rooted_tree_file tree.nwk \
  --foreground foreground.txt

Related pages

• Installation and test run
• csubst doctor
• csubst search