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# `diverse-seq` provides alignment-free algorithms to facilitate phylogenetic workflows
`diverse-seq` implements computationally efficient alignment-free algorithms that enable efficient prototyping for phylogenetic workflows. It can accelerate parameter selection searches for sequence alignment and phylogeny estimation by identifying a subset of sequences that are representative of the diversity in a collection. We show that selecting representative sequences with an entropy measure of *k*-mer frequencies correspond well to sampling via conventional genetic distances. The computational performance is linear with respect to the number of sequences and can be run in parallel. Applied to a collection of 10.5k whole microbial genomes on a laptop took ~8 minutes to prepare the data and 4 minutes to select 100 representatives. `diverse-seq` can further boost the performance of phylogenetic estimation by providing a seed phylogeny that can be further refined by a more sophisticated algorithm. For ~1k whole microbial genomes on a laptop, it takes ~1.8 minutes to estimate a bifurcating tree from mash distances.
You can read more about the methods implemented in `diverse-seq` in the preprint [here](https://biorxiv.org/cgi/content/short/2024.11.10.622877v1).
The user documentation [is here](https://diverse-seq.readthedocs.io).
### Installation
We recommend installing `diverse-seq` from PyPI as follows
```
pip install "diverse-seq[extra]"
```
for the full jupyter experience.
For command line only usage, install as follows
```
pip install diverse-seq
```
> **NOTE**
> If you experience any errors during installation, we recommend using [uv pip](https://docs.astral.sh/uv/). This command provides much better error messages than the standard `pip` command. If you cannot resolve the installation problem, please open an issue on the [GitHub repository](https://github.com/HuttleyLab/DiverseSeq/issues).
#### Using `uv`
Speaking of `uv`, it provides a simplified approach to install `dvs` as a command-line only tool as
```
uv tool install diverse-seq
```
Usage in this case is then
```
uvx --from diverse-seq dvs
```
#### Dependencies
For a full listing of dependencies, see the [pyproject.toml](./pyproject.toml) file.
### The command line interface
`dvs` is the command line interface for `diverse-seq`.
<details>
<summary>The `dvs` subcommands</summary>
<!-- [[[cog
import cog
from diverse_seq.cli import main
from click.testing import CliRunner
runner = CliRunner()
result = runner.invoke(main, [])
help = result.output.replace("Usage: main", "Usage: dvs")
cog.out(
"```\n{}\n```".format(help)
)
]]] -->
```
Usage: dvs [OPTIONS] COMMAND [ARGS]...
dvs -- alignment free detection of the most diverse sequences using JSD
Options:
--version Show the version and exit.
--help Show this message and exit.
Commands:
demo-data Export a demo sequence file
prep Writes processed sequences to a <HDF5 file>.dvseqs.
max Identify the seqs that maximise average delta JSD
nmost Identify n seqs that maximise average delta JSD
ctree Quickly compute a cluster tree based on kmers for a collection...
```
<!-- [[[end]]] -->
</details>
### The Python API
We make comparable capabilities available as [cogent3 apps](https://cogent3.org/doc/app/index.html). The main difference is the app instances directly operate on, and return, `cogent3` sequence collections. See [the docs](https://diverse-seq.readthedocs.io/en/latest/apps/) for demonstrations of how to use the apps.
## Project Information
`diverse-seq` is released under the BSD-3 license. If you want to contribute to the `diverse-seq` project (and we hope you do! :innocent:) the code of conduct and other useful developer information is available on the [wiki](https://github.com/HuttleyLab/DiverseSeq/wiki).
Raw data
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