Introduction


EzAAI is a suite of workflows for improved AAI calculation performance along with the novel module that provides hierarchical clustering analysis.

Tutorial Download GitHub Forum Cite us

Available modules


Extract

Extracts profile DB from genome using Prodigal

java -jar EzAAI.jar extract -i <IN> -o <OUT>

Argument Description
-i Input bacterial genome sequence
-o Output profile database

Convert

Converts CDS FASTA file into profile DB

java -jar EzAAI.jar convert -i <IN> -s <SEQ> -o <OUT>

Argument Description
-i Input CDS profile (FASTA format)
-s Sequence type of input file (nucl/prot)
-o Output profile DB

Calculate

Calculate AAI value from profile databases using MMseqs2

java -jar EzAAI.jar calculate -i <IN_1> -j <IN_2> -o <OUT>

Argument Description
-i First input profile DB / directory with profile DBs
-j Second input profile DB / directory with profile DBs
-o Output result file

Cluster

Hierarchical clustering of taxa with AAI values

java -jar EzAAI.jar cluster -i <IN> -o <OUT>

Argument Description
-i Input EzAAI result file containing all-by-all pairwise AAI values
-o Output result file

EzAAI TEAM

Contributors

CA

Dongwook Kim1,2
Sein Park1,2
Jon Jongsik Chun1,2,3

1 Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, Republic of Korea

2 Institute of Molecular Biology and Genetics, Seoul National University, Seoul 00826, Republic of Korea

3 School of Biological Sciences, Seoul National University, Seoul 00826, Republic of Korea