ez-convphase is a wrapper for phasing ragged FASTA alignments using itaxotools ConvPhase (implements SeqPhase and PHASE2.1). Cleans headers, masks any problematic columns, runs ConvPhase in parallel, then rebuilds the original alignment around the phased positions (column-for-column). Supports standard, Haploview & MolD header styles. TSV functions not supported at this time.
Not affiliated with iTaxoTools/ConvPhase/PHASE.
- Alignments can contain tri-allelic, missing and gap characters, which are not supported by ConvPhase's conservative input requirements.
- The scripts in this wrapper remove columns with prohibited characters and replaces them after phasing, restoring the original alignment length.
ez-convphasedoes: sanitize → phase → rebuild — and preserves your IDs.
- EZ-ConvPhase now includes a user-friendly GUI for easier pipeline management.
pip install -r requirements.txt
- Ensure system dependencies
- macOS: brew install parallel
- Ubuntu: sudo apt-get install parallel
- Header-safe: works with
sample|Speciesandsample.Species. - Hap suffix mapping on the left token only:
_a/_b,-a/-b,.a/.b,/a,/b, space-a/b, trailinga/b. - Exact reconstruction via JSON mask (
kept_indices+ per-column chars). - Parallel ConvPhase runs (GNU
parallel). - Clear logs; per-stage outputs.
GNU parallel
- macOS:
brew install parallel - Debian/Ubuntu:
sudo apt-get update && sudo apt-get install -y parallel
ConvPhase (from iTaxoTools)
- Get the ConvPhase CLI/binary from the iTaxoTools release for your OS.
- Ensure the binary (often
itaxotools-convphaseorconvphase) is on yourPATH, or set its path in the script viaCONVPHASE_BIN.
ConvPhase (CLI)
- Install from PyPI:
python -m pip install itaxotools-convphase - Command: convphase (or python -m itaxotools.convphase as a fallback)
- If you keep a local folder/binary (e.g., ConvPhase CLI/convphase), set CONVPHASE_BIN to that path
Self-check:
"${CONVPHASE_BIN:-convphase}" -h >/dev/null 2>&1
|| echo "ConvPhase CLI not found. Install with 'python -m pip install itaxotools-convphase' or set CONVPHASE_BIN to your binary."