README.md

Builds an amino acid alignment in a reference-free, alignment-free manner from a set of proteomes. Not ‘better’ than traditional marker-based pipelines, but simpler and much faster to run. Typical usages range from between-strains to within-family (prokaryotes) or within-phylum (eukaryotes) phylogenetic analyses.

Installation

You can either compile the code locally using rustc, or install a precompiled binary from Bioconda:

conda install bioconda::kamino

Usage

input

Input consists of proteome files in FASTA format (gzipped or not), with one file per sample. Files can be placed in a single directory, specified with the -i argument. Files are then recognised by their extension (.fa, .fas, .fasta, .faa, .fna; gzipped ot not) and filenames minus extensions become isolate names in the final alignment.

kamino -i <input_dir> -t 4

Alternatively , the path of input files can be provided in a headless tab-delimited file using the -I argument. This is useful when file names do not encode the sample name or when proteomes are located in multiple directories.

kamino -I <tabular_file> -t 4

The first column of the tab-delimited file should contain the isolate names in the final alignment and the second column the path of proteome files.

species_soil    new_assemblies/proteins.fas.gz
ncbi_species_1    ncbi/GCA_00076868/proteome.fa.gz
ncbi_species_2    ncbi/GCA_01092864/proteome.fa.gz

For bacterial isolates, the phylogenomic alignment can also be generated directly from genome assemblies by selecting the --genomes argument, using either -i or -I. In this case, an ultra-fast but approximate protein prediction is performed, with predicted proteomes stored in a temporary directory.

kamino -i <input_dir> -t 4 --genomes

output

kamino outputs a FASTA amino acid alignment, a file containing the percentage of missing data per isolate, and a file containing variant group coordinates in the FASTA alignment. By default, these output files use the prefix 'kamino_', but this can be changed with the -o argument.

Additionally, a Neighbour-joinging tree can be generated together with other output files by selecting the --NJ optional argument.

kamino -i <input_dir> -t 4 --NJ

Documentation

More information are available at https://docs.rs/kamino-cli/latest/kamino_cli/

Please let me know if anything is unclear or missing, and I'll update the doc accordingly.

Citation

If you use kamino, please cite:

Romain Derelle, John A. Lees and Leonid Chindelevitch. 2026. kamino: proteome-wide variant calling for amino acid phylogenomics. https://www.biorxiv.org/content/10.64898/2026.05.21.726148v1

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This codebase is provided under the MIT License. Some parts of the code were drafted using AI assistance.