EzAAI: High Throughput Prokaryotic AAI Calculator
EzAAI is a suite of workflows for improved AAI calculation performance along with the novel module that provides hierarchical clustering analysis and dendrogram representation.
Quick start with conda
conda install -c bioconda -y ezaai
ezaai -h
Available modules
extract
- Extract protein database from genome using Prodigal
ezaai extract -i <IN_SEQ> -o <OUT_DB>
| Argument |
Description |
-i |
Input prokaryotic genome sequence |
-o |
Output database |
calculate
- Calculate AAI value from protein databases using MMseqs2
ezaai calculate -i <INPUT_1> -j <INPUT_2> -o <OUTPUT>
| Argument |
Description |
-i |
First input DB / directory with DBs |
-j |
Second input DB / directory with DBs |
-o |
Output result file |
convert
- Convert CDS FASTA file into MMseqs2 database
ezaai convert -i <IN_CDS> -s <SEQ_TYPE> -o <OUT_DB>
| Argument |
Description |
-i |
Input CDS profile (FASTA format) |
-s |
Sequence type of input file (nucl/prot) |
-o |
Output database |
cluster
- Hierarchical clustering of taxa with AAI values
ezaai cluster -i <AAI_TABLE> -o <OUTPUT>
| Argument |
Description |
-i |
Input EzAAI result file containing all-by-all pairwise AAI values |
-o |
Output result file |