Unicore is a method for scalable and accurate phylogenetic reconstruction with structural core genes, universally applicable to any given set of taxa.
We will provide a Conda package soon. Please wait for the release.
Note: We will provide an easier way to download these as a
downloadmodule soon. Until then, please follow the steps below.
Please install the latest version of Rust from here.
To run createdb module, you have to pre-download the model weight of the ProstT5.
Please download the model from here.
Foldseek can be installed from here.
Default tool for MSA is Foldmason and for phylogeny inference is IQ-TREE. You can download Foldmason from here and IQ-TREE from here.
With these tools installed, you can install and run unicore by:
git clone https://github.com/steineggerlab/unicore.git
cd unicore
cargo build --release
target/release/unicore help
Unicore has four main modules:
createdb- Create 3Di structural alphabet database from input speciessearch- Search structures against given reference databaseprofile- Taxonomic profiling and core gene identificationtree- Phylogenetic inference using structural core genes
Run each module with unicore <module> help to see the detailed usage.
createdb module takes a folder with input species and outputs 3Di structural alphabets predicted with ProstT5.
This module runs much faster with GPU. Please install cuda for GPU acceleration.
Note. Currently, proteomes in
.fastaformat are only supported as an input. Eventually, we will support more types and formats that can represent species' protein space.
Example dataset:
data/
└─┬ Proteome1.fasta
├ Proteome2.fasta
...
└ ProteomeN.fasta
To run the module, please use the following command:
unicore createdb data db/proteome_db /path/to/prostt5/model
This will create a Foldseek database in the db folder.
search module takes a createdb output database, searches them against the given reference database, and outputs the alignment results in BLAST format.
On default, alignments with 80% bidirectional coverage with E-value <
Example command:
unicore search db/proteome_db /path/to/reference/db search/result tmp
This will create a result.m8 output file in the search folder.
profile module takes the database (createdb output) and alignment results (search output) to find structural core genes.
On default, the module will report the genes that are present in 80% of the species as a single copy. You can change this threshold by -t option.
Example command:
// 85% coverage
unicore profile -t 85 db/proteome_db search/result.m8 result
This will create a result folder with the core genes and their occurrence in the species.
tree module takes the core genes and the species proteomes to infer the phylogenetic tree using the alignments of the structural core genes.
On default, alignment will be generated by foldmason and truncated by 50% gap filtering, followed by phylogenetic inference using iqtree.
Example command:
unicore tree db/proteome_db result tree
This will create a tree folder with the phylogenetic tree in Newick format.