corgias 0.1.0

Phylogenetic profiling tool for identifying co- and anti-correlated orthologs in large-scale prokaryotic genome datasets

Corgias

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CORGIAS

CORrelated Genes Identifier by considering Ancestral State

CORGIAS is a phylogenetic profiling tool for a large-scale dataset comprising of thousands and tens of thousands of orthologs and genomes. As co- and anti-correlated orthologs are expexted to be functionally related, CORGIAS can help functional annotation of orthologs, especially those showing no sequence similarity to functionally known genes.

Platform Support

Feature	Linux	macOS
Core functionality	✓	✓
Polars acceleration	✓	✓
CuPy GPU acceleration	✓ (NVIDIA GPU required)	✗

Installation

# Download
git clone https://github.com/ynishimuraLv/corgias.git
cd corgias

# Create the virtual environment (Optional, but recommended)
python -m venv .venv
. .venv/bin/activate

# For System with GPU compatible CUDA 12.x
# This option is not available on macOS.
python -m pip install .[gpu]

# For System without a compatible GPU (CPU-only)
python -m pip install .

Usage at a glance

Detailed usage is discreibed here

Ancestral state reconstruction

# Reconstruct by a maximum-likelihood method
corgias asr -t samples/archaea_hq90.tre -d samples/archaea_COG_table99.csv -i 0  \
            --work_dir ML_result -c 4 --prediction_method ML --test 5

# Reconstruct by a maximum-parsimony method
corgias asr -t samples/archaea_hq90.tre -d samples/archaea_COG_table99.csv -i 0  \
            --work_dir MP_result -c 4 --prediction_method MP --test 5

Phylogenetic profiling

# naime method
corgias profiling -m naive -og samples/archaea_COG_table99.csv \
                  -o naive_test.csv -c 4 --test 5

# run lenth encoding (RLE)
corgias profiling -m rle -og samples/archaea_COG_table99.csv \
                  -t samples/archaea_hq90.tre -o rle_test.csv -c 4 --test 5

# clade-wise adjustment (CWA)
corgias profiling -m cwa -og samples/archaea_COG_table99.csv \
                  -t samples/archaea_hq90.tre -o cwa_test.csv -c 4  --test 5

# ancestral state adjustment (ASA)
corgias profiling -m asa -a ML_result -t samples/archaea_hq90.tre -o asa_test.csv -c 4 --test 5

# cotransitions (cotr)
corgias profiling -m cotr -og samples/archaea_COG_table99.csv -t samples/archaea_hq90.tre -o cotr_test.csv -c 4 --test 5

# simultaneous evolution test (SEV)
corgias profiling -m sev -a MP_result -t samples/archaea_hq90.tre -o sev_test.csv -c 4 --test 5

Statistical test

corgias stat -i naive_test.csv -m naive -o stat_naive.csv -c 4
corgias stat -i rle_test.csv -m rle -o stat_rle.csv -c 4
corgias stat -i cwa_test.csv -m cwa -o stat_cwa.csv -c 4
corgias stat -i asa_test.csv -m asa -o stat_asa.csv -c 4
corgias stat -i cotr_test.csv -m cotr -o stat_cotr.csv -c 4
corgias stat -i sev_test.csv -m sev -o stat_sev.csv -c 4

License

This project is licensed under the GPL3.0 License. See the LICENSE file for details.

Citation

If you use CORGIAS in your research, please the paper below:

Yuki Nishimura, Kimiho Omae, Kento Tominnaga, Wataru Iwasaki.
CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset
NAR Genomics and Bioinformatics, 2025, https://doi.org/10.1093/nargab/lqaf182

The results in this paper can be reproduced by using the code here

Contact

Yuki Nishimura (The University of Tokyo) [e-mail]