A Python package for converting TEI XML collations to NEXUS and other formats.
Textual scholars have been using phylogenetics to analyze manuscript traditions since the early 1990s.
Many standard phylogenetic software packages accept as input the NEXUS file format.
The teiphy program takes a collation of texts encoded using the Text Encoding Initiative (TEI) guidelines
and converts it to a NEXUS format so that it can be used for phylogenetic analysis.
It can also convert to other formats as well, including Hennig86 (for TNT), PHYLIP (for RAxML), FASTA, and the XML format used by BEAST 2.7.
Contents:
- Quickstart
- Advanced Usage
- Analysis at Varying Levels of Detail Using Reading Types
- Ambiguities and Judgments of Certainty
- Lacunae and Other Missing Data
- Correctors’ Hands
- Excluding Fragmentary witnesses
- Removing First-hand Siglum Suffixes and Merging Multiple Attestations
- Ascertainment Bias
- Tree Priors, Clock Models, and Tip Dates
- Root Frequencies and Substitution Models
- Logging for Ancestral State Reconstructions
- Overriding or Supplying Dates from a CSV file
- Supported Output Formats and Options
- Other Options
- Example
- API Reference
- Command Line Interface Reference
- Credits