目录
- .githubfix: fix typing issues2个月前
- ExampleDatadocs: update the figures and add comments on indexing1年前
- docsrefactor: update helpinfo and figures3个月前
- srcrefactor: update recur to v1.1.02个月前
- testsfix: fix the test path3个月前
- .dockerignorerefactor: add docker files1年前
- .gitignorefix: fix the syntax error2个月前
- Dockerfilefix: fix typing issues2个月前
- LICENSEfeat: remove the iqtree2 binary1年前
- MANIFEST.infix: fix typing issues2个月前
- Makefilefix: fix typing issues2个月前
- README.mdrefactor: update helpinfo and figures3个月前
- badge-status.jsonUpdate badge status3个月前
- config.jsonfeat: add user defined iqtree cmd file1年前
- pyproject.tomlfix: fix typing issues2个月前
- recur.pyfix: fix the start method issue regarding subprocesses1年前
- requirements.txtrefactor: build multi-stage-recur into RECUR10个月前
- requirements_dev.txtfeat: remove the iqtree2 binary1年前
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RECUR
Finding Recurrent Substitutions from Multiple Sequence Alignments
Introduction
The required input is either a protein or codon multiple sequence alignment (in FASTA format) and a defined outgroup species or clade. The output of RECUR is a list of recurrent amino acid substitutions (file suffix:
.recur.tsv), that have occurred in the inferred phylogeny. Outputs of intermediate steps, i.e. model selection, tree inference, ancestral state reconstruction and site substitution matrices, can be found in the.recuroutput directory.Comprehensive installation and usage documentation is available on the RECUR homepage
Citations
Elizabeth HJ Robbins, Yi Liu, Steven Kelly. 2025. RECUR: Identifying recurrent amino acid substitutions from multiple sequence alignments bioRxiv.
Credits and Acknowledgements
This is a software developed by the Steven Kelly Lab.
Contributing
If you find a bug 🐛, please open a bug report. If you have an idea for an improvement or new feature, please open a feature request.