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.

• Homepage
• Publication

Quick start with conda

conda install -c bioconda ezaai
ezaai -h

Build from source

Requirements

• Java 8+
• Maven 3+

git clone https://github.com/endixk/ezaai.git
cd ezaai
mvn clean compile assembly:single
java -jar target/EzAAI-*.jar -h

Available modules

extract

• Extract protein database(s) from genome using Prodigal

ezaai extract -i <IN_SEQ> -o <OUT_DB>

|Argument|Description| |:-:|-----------------| |-i|Input file or directory with prokaryotic genome sequence(s)| |-o|Output file or directory|

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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|

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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|

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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|