https://github.com/endixk/ezaai

EzAAI - High Throughput Prokaryotic AAI Calculator
https://github.com/endixk/ezaai

comparative-genomics genomics prokaryotic-genomes proteomics

Last synced: 3 months ago
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EzAAI - High Throughput Prokaryotic AAI Calculator

• Host: GitHub
• URL: https://github.com/endixk/ezaai
• Owner: endixk
• License: gpl-3.0
• Created: 2021-02-02T07:11:37.000Z (over 4 years ago)
• Default Branch: main
• Last Pushed: 2025-07-09T15:34:37.000Z (3 months ago)
• Last Synced: 2025-07-09T16:31:21.281Z (3 months ago)
• Topics: comparative-genomics, genomics, prokaryotic-genomes, proteomics
• Language: Java
• Homepage: http://leb.snu.ac.kr/ezaai
• Size: 41.1 MB
• Stars: 42
• Watchers: 2
• Forks: 5
• Open Issues: 17
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md
  • Citation: CITATION.cff

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README

          
# EzAAI: High Throughput Prokaryotic AAI Calculator 

[![Build](https://img.shields.io/github/actions/workflow/status/endixk/ezaai/maven-build.yml)](https://github.com/endixk/ezaai/actions)

[![License](https://img.shields.io/github/license/endixk/ezaai)](https://github.com/endixk/ezaai/blob/main/LICENSE.md)

[![Bioconda](https://img.shields.io/conda/dn/bioconda/ezaai?logo=anaconda)](https://anaconda.org/bioconda/ezaai) 

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](http://leb.snu.ac.kr/ezaai)

 * [Publication](https://doi.org/10.1007/s12275-021-1154-0)

## Quick start with conda

~~~bash

conda install -c bioconda -y ezaai

ezaai -h

~~~

## Available modules

### `extract`

 * Extract protein database from genome using Prodigal

~~~bash

ezaai extract -i  -o 

~~~

|Argument|Description|

|:-:|-----------------|

|`-i`|Input prokaryotic genome sequence|

|`-o`|Output database|

---

### `calculate`	

 * Calculate AAI value from protein databases using MMseqs2

~~~bash

ezaai calculate -i  -j  -o 

~~~

|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

~~~bash

ezaai convert -i  -s  -o 

~~~

|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

~~~bash

ezaai cluster -i  -o 

~~~

|Argument|Description|

|:-:|-----------------|

|`-i`|Input EzAAI result file containing all-by-all pairwise AAI values|

|`-o`|Output result file|