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