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Welcome to the HaMStR-oneSeq wiki!
HaMStR-oneSeq is a feature-aware orthology prediction tool. For a single seed sequence, HaMStR-oneSeq can find its orthologs and co-orthologs from different strains of the seed species or from distantly related taxa to draw the complete picture about the evolutionary history of the sequence of interest. HaMStR-oneSeq is distributed as a python package called h1s. It is compatible with Python ≥ v3.7.
HaMStR-oneSeq integrates the prediction of orthologs and the calculation of the Feature Architecture Similarty (FAS) scores. FAS scores are computed pairwise between the query gene and it's predicted orthologous genes using FAS tool, which will be automatically installed during the setup of h1s package. Combining both sequence similarity and feature architecture similarity, HaMStR-oneSeq results are suitable for analysing not only the sequences themselves but also their functions throughout the evolution.
In this wiki, you will find how to
- Install HaMStR-oneSeq and its dependencies
- Use the standalone version as well as the central installed version
- Add new taxa to HaMStR-oneSeq
- Check the validity of your data for running HaMStR-oneSeq
- Merge outputs of several HaMStR-oneSeq run into one single output
Besides, we provide also a quick-and-dirty explanation of how h1s works, a detailed information of the input and output files, some specific use-cases of HaMStR-oneSeq and a FAQ section.
If this wiki cannot help you with your issue, please contact us! We are very happy to hear from your ;)