kamino-cli
| Crates.io | kamino-cli |
| lib.rs | kamino-cli |
| version | 0.5.0 |
| created_at | 2026-01-14 18:45:15.41119+00 |
| updated_at | 2026-01-20 15:36:59.593284+00 |
| description | Build phylogenomic datasets in seconds. |
| homepage | |
| repository | https://github.com/rderelle/kamino |
| max_upload_size | |
| id | 2043442 |
| size | 141,462 |
Romain Derelle (rderelle)
documentation
README
From the Spanish word for path.
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 faster to run.
Typical usages range from between-species to within-phylum phylogenetic analyses (bacteria, archaea and eukaryotes).
under the hood
kamino performs the following successive steps:
- lists proteome files from the input directory (-i or -I)
- recodes proteins with a 6-letters recoding scheme (-r)
- simplifies proteomes by discarding out-branching k-mers
- builds a global assembly graph and identifies variant groups as described here (-d)
- converts variant group paths back to amino acids using a sliding window
- mask long polymorphism runs within variant groups (-m)
- filters variant groups by missing data and middle-length thresholds (-f and -l)
- extracts middle positions and incorporate 'constant' positions (-c)
- outputs the final amino acid alignment (-o)
installation
You can either compile the code locally using rustc, or install a precompiled binary from Bioconda:
conda install bioconda::kamino
running kamino
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), or their paths can be provided in a tab-delimited file using -I.
A basic run using four threads can be performed with either of the following commands:
kamino -i <input_dir> -t 4
kamino -I <tabular_file> -t 4
examples
All analyses were performed on a MacBook "M4 Pro" using v0.4.0 and 4 threads (other parameters set to default unless specified):
| dataset | taxonomic diversity | runtime (min) | memory (GB) | alignment size (aa) |
|---|---|---|---|---|
| 50 Mycobacterium | within-genera | 0.1 | 2 | 19,283 |
| 400 Mycobacterium | within-genera | 0.9 | 8 | 13,753 |
| 50 Polyporales (fungi) | within-order | 0.5 | 8 | 21,808 |
| 46 Drosophila | within-genera | 0.7 | 7 | 194,021 |
| 55 Mammalia | within-class | 1.6 | 14 | 291,437 |
55 Mammalia -k 13 |
within-class | 1.9 | 8 | 191,962 |
FAQ
-
When not to use kamino?
- low diversity datasets (ie, within-species), for which genome-based approaches will be more powerful
- very large datasets (eg, thousands of bacterial proteomes or hundreds of vertebrate proteomes)
- very divergent datasets (eg, animal kingdom)
- distant outgroup composed of a few isolates: these might have disproportionately more missing data
- list to be completed ...
-
Is the output reproducible?
Yes, kamino is fully deterministic so will produce the exact same alignment for a given version, set of parameters and input proteomes.
- How to get more phylogenetic positions?
Increase the k-mer size (-k), increase the maximum depth of the graph traversal (-d), or lower the minimum proportion of isolates with amino acid per position (-m) if that is acceptable for downstream analyses.
This codebase is provided under the MIT License. Some parts of the code were drafted using AI assistance.