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.

You can read more about the methods implemented in diverse-seq in the published article.

Warning

We have rewritten a substantial part of the project in Rust. We now also use the Zarr storage format instead of HDF5. As a result, the output file from dvs prep now has the suffix .dvseqsz instead of .dvseq. Old-format files are not compatible with this version.

Installation

diverse-seq can be installed from PyPI as follows

pip install diverse-seq

Note

If you experience any errors during installation, we recommend using uv pip. This command provides much better error messages than the standard pip command. If you cannot resolve the installation problem, please open an issue.

The extra install option

To get the additional components for working within Jupyter notebooks, or just to reproduce all the examples in the documentation, do the install as follows

pip install "diverse-seq[extra]"

Installation and usage with uv

Speaking of uv, it provides a simplified approach to install dvs as a command-line only tool as

uv tool install diverse-seq

For the examples in this documentation, you can access the dvs command as

uvx --from diverse-seq dvs

without having to activate a virtual environment.