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EzAAI: High Throughput Prokaryotic AAI Calculator \n[![Build](https://img.shields.io/github/actions/workflow/status/endixk/ezaai/maven-build.yml)](https://github.com/endixk/ezaai/actions)\n[![License](https://img.shields.io/github/license/endixk/ezaai)](https://github.com/endixk/ezaai/blob/main/LICENSE.md)\n[![Bioconda](https://img.shields.io/conda/dn/bioconda/ezaai?logo=anaconda)](https://anaconda.org/bioconda/ezaai) \n\nEzAAI is a suite of workflows for improved AAI calculation performance along with the novel module that provides hierarchical clustering analysis and dendrogram representation.\n\n * [Homepage](http://leb.snu.ac.kr/ezaai)\n * [Publication](https://doi.org/10.1007/s12275-021-1154-0)\n\n\n## Quick start with conda\n\n~~~bash\nconda install -c bioconda -y ezaai\nezaai -h\n~~~\n\n## Available modules\n### `extract`\n * Extract protein database from genome using Prodigal\n\n~~~bash\nezaai extract -i \u003cIN_SEQ\u003e -o \u003cOUT_DB\u003e\n~~~\n\n|Argument|Description|\n|:-:|-----------------|\n|`-i`|Input prokaryotic genome sequence|\n|`-o`|Output database|\n\n---\n\n### `calculate`\t\n * Calculate AAI value from protein databases using MMseqs2\n\n~~~bash\nezaai calculate -i \u003cINPUT_1\u003e -j \u003cINPUT_2\u003e -o \u003cOUTPUT\u003e\n~~~\n\n|Argument|Description|\n|:-:|-----------------|\n|`-i`|First input DB / directory with DBs|\n|`-j`|Second input DB / directory with DBs|\n|`-o`|Output result file|\n\n---\n\n### `convert`\t\n * Convert CDS FASTA file into MMseqs2 database\n\n~~~bash\nezaai convert -i \u003cIN_CDS\u003e -s \u003cSEQ_TYPE\u003e -o \u003cOUT_DB\u003e\n~~~\n\n|Argument|Description|\n|:-:|-----------------|\n|`-i`|Input CDS profile (FASTA format)|\n|`-s`|Sequence type of input file (nucl/prot)|\n|`-o`|Output database|\n\n---\n\n### `cluster`\n * Hierarchical clustering of taxa with AAI values\n\n~~~bash\nezaai cluster -i \u003cAAI_TABLE\u003e -o \u003cOUTPUT\u003e\n~~~\n\n|Argument|Description|\n|:-:|-----------------|\n|`-i`|Input EzAAI result file containing all-by-all pairwise AAI values|\n|`-o`|Output result file|\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fendixk%2Fezaai","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fendixk%2Fezaai","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fendixk%2Fezaai/lists"}