Cactus-RaMAx helps you remix alignment plans emitted by cactus-prepare. You can inspect every round, toggle RaMAx for any subtree, and then run or export the resulting command list. The current version (0.4.0) keeps the ASCII phylogenetic canvas with subtree/single-node toggle scopes, search, proportional branch spacing, and a bottom HUD that summarizes the current node, coverage, and live system metrics. Subtree Mode is a CAX-only toggle that disables descendant RaMAx automatically and gracefully reverts if you later edit a child node.

We recommend creating a fresh Conda environment and installing the project in editable mode:

conda create -n cax python=3.10 -y
conda activate cax

pip install -e .

Alternatively, you can build a wheel and install it in a different environment:

python -m build
pip install dist/cactus_ramax-*.whl

Run the entry point directly:

cax

• If you do not pass --prepare-args or --from-file, a Textual prompt opens so you can type or assemble a full cactus-prepare command.
  • Press F2 (or type :wizard) to open the argument wizard and fill --outDir, --outSeqFile, --outHal, and --jobStore one field at a time.
  • Press F3 (or type :template) to choose from Evolver examples bundled with the package or from your own ~/.cax/templates.json.
  • Press F4 or type !N (for example !1) to recall the Nth entry from ~/.cax/history.json. The prompt keeps the 20 most recent commands and lets you delete entries from the history window.
• Before running cactus-prepare, CAX infers the effective output directory (from --outDir or the parent directory of --outSeqFile) and offers to delete existing --outDir/--jobStore paths so the run starts cleanly.
• If logs/run_state.json is present and you choose to keep existing outputs, the UI opens directly into a resume view (inside Run Settings) showing which steps can be skipped, which will rerun, and where execution resumes.
• After execution completes, the UI displays the parsed plan and lets you toggle RaMAx replacements before running or exporting.
• Scripted usage is still supported:

  cax --prepare-args "examples/evolverMammals.txt --outDir steps-output --outSeqFile ... --outHal ... --jobStore jobstore"

  or load an existing output:

  cax --from-file steps-output/prepare_output.txt

• Pass --threads 32 to seed the run-settings prompt so cactus steps inherit --maxCores 32 and RaMAx receives --threads 32; leave it unset to default to each command's original flag.

• The left pane renders an ASCII phylogenetic canvas with proportional branch spacing; use arrow keys or h/j/k/l to move, press Space to toggle RaMAx using the current scope, and press b to switch the scope between subtree and single node. Press / to search node names, then n / Shift+N to cycle through matches.
• The canvas paints cactus vs. RaMAx states inline, annotates branch lengths on dotted leaders, and shows a bottom HUD with identity, subtree/total RaMAx coverage, and live CPU/GPU/memory/disk metrics. Press i for a full detail modal of the current node.
• E: edit commands for the selected round or RaMAx replacement in a multi-line editor (press Ctrl+S to save).
• R: open the Run Settings screen to review verbose logging and the shared thread count, run the plan, or save the generated command list. The screen is fully keyboard-driven (Tab / Shift+Tab, Ctrl+Enter, V), and F6 switches between the classic plan overview and a new flow view that renders the execution dependency tree in ASCII.
• Q: quit the UI.
• Verbose streaming is only controlled via the run-settings dialog so you can review the choice right before execution.

When RaMAx is enabled for a round or subtree, execution stops on the first failure—it does not fall back to cactus blast/align automatically.

• Built-in templates are sourced from the packaged Evolver mammals/primates examples and any .txt files you add under examples/; user-defined templates live in ~/.cax/templates.json.
• Command history is stored at ~/.cax/history.json. It deduplicates consecutive runs, keeps up to 20 entries, and syncs with the Textual prompt so you can reuse or delete past commands.

• The raw output from cactus-prepare is stored at <out_dir>/cax_prepare_debug.txt. If you only passed --outSeqFile, the parent directory of that file becomes the inferred output directory.
• Runtime logs reuse the directories referenced by the original plan, for example steps-output/logs/.
• Command history and templates live under ~/.cax/ so you can reuse them across projects or machines.

Open an issue or pull request to help us iterate on the combined Cactus/RaMAx workflow.