Troubleshooting
Start with the command's canonical reference page and its live interface:
phykit <command> --help
Installation and command discovery
Confirm that PhyKIT and the active Python interpreter come from the same environment:
python -m pip show phykit
command -v phykit
phykit version
If phykit is not found, activate the environment used for installation or
run python -m pip install --upgrade phykit in the intended environment.
PhyKIT requires Python 3.10 or newer.
Input and parsing errors
Resolve relative paths from the current working directory. Use absolute paths when an input list refers to files outside that directory.
Ensure FASTA records have unique identifiers and aligned sequences have equal lengths.
Ensure Newick trees end with a semicolon and every required tip has a name.
Match taxon names exactly across files. Capitalization, spaces, and underscores are significant.
Use tab characters, rather than runs of spaces, in documented TSV inputs.
Preserve the documented header or no-header convention for each command.
Unexpected or empty results
Check filters, thresholds, missing-data rules, and taxon intersections before
changing the analysis. An empty result can be valid when no site, split, taxon,
or model satisfies the selected criteria. Use --json where available to
distinguish an empty structured result from formatting intended for people.
Reproducibility
Record the output of phykit version, the complete command, input checksums,
and random seed. Commands that expose --seed should use an explicit value in
reproducible workflows. Do not assume defaults are unchanged across releases;
consult the versioned command catalog.
Reporting a problem
Open a GitHub issue with the PhyKIT and Python versions, operating system, complete command, full error text, and a minimal input that reproduces the problem. Remove sensitive data before attaching files.