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haeussma authored Feb 19, 2024
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</div>

[![Generate API](https://github.com/PyEED/pyeed/actions/workflows/generate_api.yaml/badge.svg)](https://github.com/PyEED/pyeed/actions/workflows/generate_api.yaml)
[![Tests](https://github.com/PyEED/pyeed/actions/workflows/tests.yaml/badge.svg)](https://github.com/PyEED/pyeed/actions/workflows/tests.yaml)
[![Documentation](https://github.com/PyEED/pyeed/actions/workflows/make_docs.yaml/badge.svg)](https://github.com/PyEED/pyeed/actions/workflows/make_docs.yaml)

## About 📖
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## Installation ⚙️

Install pyEED by running
Install `pyeed` by running
```bash
pip install git+https://github.com/PyEED/pyeed.git
```
... or update pyEED to get the latest features.
```bash
pip install --upgrade git+https://github.com/PyEED/pyeed.git
```

## Quick start 🚀

In the following example, information of the [aldolase](https://www.ncbi.nlm.nih.gov/protein/NP_001287541.1/) (*Drosophila melanogaster*) is retrieved from the corresponding GenBank entry. Thereafter, a protein blast search ist started and the found sequence information is fetched and stored as `ProteinSequence` objects.

```python
from pyEED.core import ProteinInfo
from pyeed.core import ProteinInfo

# Get a protein entry from NCBI by accession id
aldolase = ProteinInfo.from_ncbi("NP_001287541.1")
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## Documentation 📘

Check out the [documentation](https://pyeed.github.io/pyeed/) for in-depth information on how to setup PyEED,
Check out the [documentation](https://pyeed.github.io/pyeed/) for in-depth information on how to setup `pyeed`,
use the build-in tools, and store sequence data in databases.
Documentation is in the making 🐛

## Roadmap 🛣️

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- [x] Running pairwise alignments
- [x] Network analysis / visualization
- [ ] Create phylogenetic trees
- [ ] Multi-sequence alignments
- [x] Multi-sequence alignments
- [ ] Representative clustering

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