/ezaai

EzAAI - High Throughput Prokaryotic AAI Calculator

Primary LanguageJavaGNU General Public License v3.0GPL-3.0

EzAAI: High Throughput Prokaryotic AAI Calculator

Build License Bioconda

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