- COATi has 6 available commands:
help,alignpair- pairwise alignment,msa- multiple sequences alignment (in development),sample- align two sequences and sample alignments,genseed- generate a random seed, andformat- convert format, extract and/or reorder sequences. coati alignpaircan now use five different models: tri-mg (triplet Muse and Gaut), mar-mg (marginal Muse and Gaut), tri-ecm (Empirical Codon Model), mar-ecm (marginal ECM), and dna.- Input and output formats now include FASTA, PHYLIP, and JSON.
- COATi reads from stdin and writes to stdout (in JSON format) by default.
- Users can now specify parameter values. For an up-to-date list of parameters
run
coati-command --help. - Ambiguous nucleotides on descendant sequence are supported.
- Add doxygen documentation.
- FSTlib, CLI, and doctest dependencies are now included and built with COATi as static libraries.
- Eigen, JSON library, and Google Benchmark are handled by Meson (via meson wrapDB).
- Initial Release
coati versionreturns the version informationcoati alignpair -f fasta.fas -m toycoatialigns two sequences given in a FASTA formatted file using toycoati model.
- This release focused on setting up the project infrastructure including unit testing, continuous integration, code formatting, and code analysis.