# MiGA Manual

## main

- [Introduction](https://manual.microbial-genomes.org/intro.md)
- [Part I: What is MiGA?](https://manual.microbial-genomes.org/part1.md)
- [How can MiGA help me?](https://manual.microbial-genomes.org/part1/pitch.md)
- [Who is using MiGA?](https://manual.microbial-genomes.org/part1/use-cases.md)
- [Who is behind MiGA?](https://manual.microbial-genomes.org/part1/contributors.md)
- [Definitions](https://manual.microbial-genomes.org/part1/glossary.md)
- [Part II: Getting started](https://manual.microbial-genomes.org/part2.md)
- [Requirements](https://manual.microbial-genomes.org/part2/requirements.md)
- [Using Homebrew](https://manual.microbial-genomes.org/part2/requirements/brew.md)
- [Using apt-get](https://manual.microbial-genomes.org/part2/requirements/apt-get.md)
- [Using Conda](https://manual.microbial-genomes.org/part2/requirements/conda.md)
- [Installing from source](https://manual.microbial-genomes.org/part2/requirements/source.md)
- [MyTaxa Utils](https://manual.microbial-genomes.org/part2/requirements/mytaxa.md)
- [Installation](https://manual.microbial-genomes.org/part2/installation.md)
- [MiGA types](https://manual.microbial-genomes.org/part2/types.md)
- [Input data](https://manual.microbial-genomes.org/part2/input.md)
- [Distances](https://manual.microbial-genomes.org/part2/distances.md)
- [Clustering](https://manual.microbial-genomes.org/part2/clustering.md)
- [Part III: Interfaces](https://manual.microbial-genomes.org/part3.md)
- [MiGA API](https://manual.microbial-genomes.org/part3/miga-api.md)
- [MiGA CLI](https://manual.microbial-genomes.org/part3/miga-cli.md)
- [MiGA Web](https://manual.microbial-genomes.org/part3/miga-web.md)
- [Part IV: Deploying examples](https://manual.microbial-genomes.org/part4.md)
- [RefSeq in MiGA](https://manual.microbial-genomes.org/part4/deploy-refseq.md)
- [Build a clade collection](https://manual.microbial-genomes.org/part4/deploy-clade.md)
- [Launching daemons](https://manual.microbial-genomes.org/part4/daemons.md)
- [Setting up MiGA in a cluster](https://manual.microbial-genomes.org/part4/cluster.md)
- [Part V: Additional details](https://manual.microbial-genomes.org/part5.md)
- [Advanced configuration](https://manual.microbial-genomes.org/part5/advanced-configuration.md)
- [MiGA workflow](https://manual.microbial-genomes.org/part5/workflow.md)
- [Metadata](https://manual.microbial-genomes.org/part5/metadata.md)
- [External Software](https://manual.microbial-genomes.org/part5/external.md)
- [Part VI: Workflows](https://manual.microbial-genomes.org/part6.md)
- [Quality](https://manual.microbial-genomes.org/part6/quality_wf.md)
- [Dereplicate](https://manual.microbial-genomes.org/part6/derep_wf.md)
- [Classify](https://manual.microbial-genomes.org/part6/classify_wf.md)
- [Preprocess](https://manual.microbial-genomes.org/part6/preproc_wf.md)
- [Index](https://manual.microbial-genomes.org/part6/index_wf.md)
- [Summaries](https://manual.microbial-genomes.org/part6/summaries.md)

## Primary version

- [Introduction](https://manual.microbial-genomes.org/master/master.md)
- [Part I: What is MiGA?](https://manual.microbial-genomes.org/master/part1.md)
- [How can MiGA help me?](https://manual.microbial-genomes.org/master/part1/pitch.md)
- [Who is using MiGA?](https://manual.microbial-genomes.org/master/part1/use-cases.md)
- [Who is behind MiGA?](https://manual.microbial-genomes.org/master/part1/contributors.md)
- [Definitions](https://manual.microbial-genomes.org/master/part1/glossary.md)
- [Part II: Getting started](https://manual.microbial-genomes.org/master/part2.md)
- [Requirements](https://manual.microbial-genomes.org/master/part2/requirements.md)
- [Using Homebrew](https://manual.microbial-genomes.org/master/part2/requirements/brew.md)
- [Using apt-get](https://manual.microbial-genomes.org/master/part2/requirements/apt-get.md)
- [Using Conda](https://manual.microbial-genomes.org/master/part2/requirements/conda.md)
- [Installing from source](https://manual.microbial-genomes.org/master/part2/requirements/source.md)
- [MyTaxa Utils](https://manual.microbial-genomes.org/master/part2/requirements/mytaxa.md)
- [Installation](https://manual.microbial-genomes.org/master/part2/installation.md)
- [MiGA types](https://manual.microbial-genomes.org/master/part2/types.md)
- [Input data](https://manual.microbial-genomes.org/master/part2/input.md)
- [Distances](https://manual.microbial-genomes.org/master/part2/distances.md)
- [Clustering](https://manual.microbial-genomes.org/master/part2/clustering.md)
- [Part III: Interfaces](https://manual.microbial-genomes.org/master/part3.md)
- [MiGA API](https://manual.microbial-genomes.org/master/part3/miga-api.md)
- [MiGA CLI](https://manual.microbial-genomes.org/master/part3/miga-cli.md)
- [MiGA Web](https://manual.microbial-genomes.org/master/part3/miga-web.md)
- [Part IV: Deploying examples](https://manual.microbial-genomes.org/master/part4.md)
- [RefSeq in MiGA](https://manual.microbial-genomes.org/master/part4/deploy-refseq.md)
- [Build a clade collection](https://manual.microbial-genomes.org/master/part4/deploy-clade.md)
- [Launching daemons](https://manual.microbial-genomes.org/master/part4/daemons.md)
- [Setting up MiGA in a cluster](https://manual.microbial-genomes.org/master/part4/cluster.md)
- [Part V: Additional details](https://manual.microbial-genomes.org/master/part5.md)
- [Advanced configuration](https://manual.microbial-genomes.org/master/part5/advanced-configuration.md)
- [MiGA workflow](https://manual.microbial-genomes.org/master/part5/workflow.md)
- [Metadata](https://manual.microbial-genomes.org/master/part5/metadata.md)
- [External Software](https://manual.microbial-genomes.org/master/part5/external.md)
- [Part VI: Workflows](https://manual.microbial-genomes.org/master/part6.md)
- [Quality](https://manual.microbial-genomes.org/master/part6/quality_wf.md)
- [Dereplicate](https://manual.microbial-genomes.org/master/part6/derep_wf.md)
- [Classify](https://manual.microbial-genomes.org/master/part6/classify_wf.md)
- [Preprocess](https://manual.microbial-genomes.org/master/part6/preproc_wf.md)
- [Index](https://manual.microbial-genomes.org/master/part6/index_wf.md)
- [Summaries](https://manual.microbial-genomes.org/master/part6/summaries.md)