Frequently asked questions

How do I choose a command?

Start with the task-oriented command reference. Each canonical page lists aliases, accepted arguments, defaults, output behavior, scientific interpretation, examples, limitations, validation, and citations.

How do I see the options for my installed version?

Run phykit <command> --help. The website documents the current release, while the local help reflects the version active in your environment.

Can PhyKIT produce machine-readable output?

Most analytical commands expose --json. Check the generated runtime table on the canonical command page. The full command and argument catalog is available as commands.json.

Why are taxa being dropped or reported as missing?

Taxon names must match exactly across inputs. Commands differ in whether they reject mismatches, use the shared intersection, or allow partial taxon sets. Read the command's missing-taxa option and the format conventions.

What alignment and tree formats are supported?

See Input formats and shared conventions. Alignment format is detected from content; tree inputs are normally Newick.

How do I make an analysis reproducible?

Record the PhyKIT version, complete command, input checksums, and explicit random seed. Keep structured JSON output when available and cite the methods identified on the command page.

How do I report a bug or request a feature?

Open a GitHub issue. For bugs, include a minimal reproducible example, complete error text, PhyKIT and Python versions, and operating system. See Troubleshooting before posting installation or input-format problems.