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Updated Bioconda information in Readme.
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agudys committed Aug 1, 2024
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# Clusty

[![Bioconda downloads](https://img.shields.io/conda/dn/bioconda/clusty.svg?style=flag&label=Bioconda%20downloads)](https://anaconda.org/bioconda/clusty)
[![GitHub downloads](https://img.shields.io/github/downloads/refresh-bio/clusty/total.svg?style=flag&label=GitHub%20downloads)](https://github.com/refresh-bio/clusty/releases)
[![GitHub Actions CI](../../workflows/GitHub%20Actions%20CI/badge.svg)](../../actions/workflows/main.yml)
[![License](https://anaconda.org/bioconda/famsa/badges/license.svg)](https://www.gnu.org/licenses/gpl-3.0.html)
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## Installation

Clusty comes with a set of precompiled binaries for Windows and Linux. They can be found under [Releases](./releases) tab.
The package can be also built from the sources distributed as:
The software is also available on [Bioconda](https://anaconda.org/bioconda/clusty):
```
conda install -c bioconda clusty
```
For detailed instructions how to set up Bioconda, please refer to the [Bioconda manual](https://bioconda.github.io/user/install.html#install-conda).

The package can be built from the sources distributed as:
* Visual Studio 2022 solution for Windows,
* MAKE project for Linux (g++-10 required).

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| CD-HIT | Greedy clustering with objects investigated in descending order w.r.t. the representativeness. Every unassigned object becomes a new centroid with all connected objects being assigned to it. Equivalent to MMseqs mode 2 clustering. | *O*(*e*) |
| Leiden | Iterative heuristic for finding communities in networks. It consists of three phases: (1) local moving of nodes, (2) refinement of the partition, and (3) aggregation of the network using the refined and the non-refined partitions. | unknown (algorithm provided by an external library) |

## Citation
Zielezinski A, Gudyś A, Barylski J, Siminski K, Rozwalak P, Dutilh BE, Deorowicz S. Ultrafast and accurate sequence alignment and clustering of viral genomes. bioRxiv [doi:10.1101/2024.06.27.601020].

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