# OrthoEvol

> This package aids in the analysis of orthologous genes.

## Docs

### API Reference

#### Ortholog discovery
> Infer orthologs and summarize comparative-genetics results.

- [Orthologs.Blast.BaseComparativeGenetics](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Blast.BaseComparativeGenetics.html)
- [Orthologs.Blast.ComparativeGenetics](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Blast.ComparativeGenetics.html)
- [Orthologs.Blast.BaseBlastN](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Blast.BaseBlastN.html)
- [Orthologs.Blast.OrthoBlastN](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Blast.OrthoBlastN.html)

#### Sequence retrieval
> Retrieve and organize GenBank records and NCBI datasets.

- [Orthologs.GenBank.GenBank](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.GenBank.GenBank.html)
- [Tools.ftp.BaseFTPClient](https://datasnakes.github.io/OrthoEvolution/reference/Tools.ftp.BaseFTPClient.html)
- [Tools.ftp.NcbiFTPClient](https://datasnakes.github.io/OrthoEvolution/reference/Tools.ftp.NcbiFTPClient.html)
- [Tools.mygene.MyGene](https://datasnakes.github.io/OrthoEvolution/reference/Tools.mygene.MyGene.html)

#### Alignment and phylogenetics
> Prepare alignments and run supported phylogenetic programs.

- [Orthologs.Align.ClustalO](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Align.ClustalO.html)
- [Orthologs.Align.Guidance2Commandline](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Align.Guidance2Commandline.html)
- [Orthologs.Align.Pal2NalCommandline](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Align.Pal2NalCommandline.html)
- [Orthologs.Align.MultipleSequenceAlignment](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Align.MultipleSequenceAlignment.html)
- [Orthologs.Phylogenetics.RelaxPhylip](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Phylogenetics.RelaxPhylip.html)
- [Orthologs.Phylogenetics.ETE3PAML](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Phylogenetics.ETE3PAML.html)
- [Orthologs.Phylogenetics.PhyML](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Phylogenetics.PhyML.html)
- [Orthologs.Phylogenetics.Phylip](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Phylogenetics.Phylip.html)
- [Orthologs.Phylogenetics.IQTreeCommandline](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Phylogenetics.IQTreeCommandline.html)
- [Orthologs.Phylogenetics.FilteredTree](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Phylogenetics.FilteredTree.html)
- [Orthologs.Phylogenetics.TreeViz](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Phylogenetics.TreeViz.html)
- [Orthologs.Phylogenetics.PAML.CodemlRun](https://datasnakes.github.io/OrthoEvolution/reference/Orthologs.Phylogenetics.PAML.CodemlRun.html)

#### Project and data management
> Create project layouts and coordinate data and database workflows.

- [Manager.management.Management](https://datasnakes.github.io/OrthoEvolution/reference/Manager.management.Management.html)
- [Manager.management.RepoManagement](https://datasnakes.github.io/OrthoEvolution/reference/Manager.management.RepoManagement.html)
- [Manager.management.UserManagement](https://datasnakes.github.io/OrthoEvolution/reference/Manager.management.UserManagement.html)
- [Manager.management.WebsiteManagement](https://datasnakes.github.io/OrthoEvolution/reference/Manager.management.WebsiteManagement.html)
- [Manager.management.ProjectManagement](https://datasnakes.github.io/OrthoEvolution/reference/Manager.management.ProjectManagement.html)
- [Manager.data_management.DataMana](https://datasnakes.github.io/OrthoEvolution/reference/Manager.data_management.DataMana.html)
- [Manager.database_management.BaseDatabaseManagement](https://datasnakes.github.io/OrthoEvolution/reference/Manager.database_management.BaseDatabaseManagement.html)
- [Manager.database_management.DatabaseManagement](https://datasnakes.github.io/OrthoEvolution/reference/Manager.database_management.DatabaseManagement.html)
- [Manager.database_dispatcher.DatabaseDispatcher](https://datasnakes.github.io/OrthoEvolution/reference/Manager.database_dispatcher.DatabaseDispatcher.html)
- [Manager.biosql.biosql.BaseBioSQL](https://datasnakes.github.io/OrthoEvolution/reference/Manager.biosql.biosql.BaseBioSQL.html)
- [Manager.biosql.biosql.SQLiteBioSQL](https://datasnakes.github.io/OrthoEvolution/reference/Manager.biosql.biosql.SQLiteBioSQL.html)
- [Manager.biosql.biosql.MySQLBioSQL](https://datasnakes.github.io/OrthoEvolution/reference/Manager.biosql.biosql.MySQLBioSQL.html)

#### Execution and supporting tools
> Run local, PBS, Slurm, logging, and transfer helpers.

- [Tools.pbs.BaseQsub](https://datasnakes.github.io/OrthoEvolution/reference/Tools.pbs.BaseQsub.html)
- [Tools.pbs.Qsub](https://datasnakes.github.io/OrthoEvolution/reference/Tools.pbs.Qsub.html)
- [Tools.pbs.BaseQstat](https://datasnakes.github.io/OrthoEvolution/reference/Tools.pbs.BaseQstat.html)
- [Tools.pbs.Qstat](https://datasnakes.github.io/OrthoEvolution/reference/Tools.pbs.Qstat.html)
- [Tools.pbs.MultiQstat](https://datasnakes.github.io/OrthoEvolution/reference/Tools.pbs.MultiQstat.html)
- [Tools.pbs.TargetJobKeyError](https://datasnakes.github.io/OrthoEvolution/reference/Tools.pbs.TargetJobKeyError.html)
- [Tools.slurm.SlurmClient](https://datasnakes.github.io/OrthoEvolution/reference/Tools.slurm.SlurmClient.html)
- [Tools.slurm.SlurmJob](https://datasnakes.github.io/OrthoEvolution/reference/Tools.slurm.SlurmJob.html)
- [Tools.slurm.SlurmCommandNotFoundError](https://datasnakes.github.io/OrthoEvolution/reference/Tools.slurm.SlurmCommandNotFoundError.html)
- [Tools.parallel.Multiprocess](https://datasnakes.github.io/OrthoEvolution/reference/Tools.parallel.Multiprocess.html)
- [Tools.logit.LogIt](https://datasnakes.github.io/OrthoEvolution/reference/Tools.logit.LogIt.html)
- [Tools.pybasher.PyBasher](https://datasnakes.github.io/OrthoEvolution/reference/Tools.pybasher.PyBasher.html)
- [Tools.send2server.S2S](https://datasnakes.github.io/OrthoEvolution/reference/Tools.send2server.S2S.html)
- [Tools.slackify.Slackify](https://datasnakes.github.io/OrthoEvolution/reference/Tools.slackify.Slackify.html)

#### Templates and utilities
> Create project templates and use shared package utilities.

- [Cookies.Oven](https://datasnakes.github.io/OrthoEvolution/reference/Cookies.Oven.html)
- [Cookies.CookBook](https://datasnakes.github.io/OrthoEvolution/reference/Cookies.CookBook.html)
- [resources.package_resource_path](https://datasnakes.github.io/OrthoEvolution/reference/resources.package_resource_path.html)
- [utilities.DuplicateAnalysis](https://datasnakes.github.io/OrthoEvolution/reference/utilities.DuplicateAnalysis.html)
- [utilities.BlastUtils](https://datasnakes.github.io/OrthoEvolution/reference/utilities.BlastUtils.html)
- [utilities.GenbankUtils](https://datasnakes.github.io/OrthoEvolution/reference/utilities.GenbankUtils.html)
- [utilities.OrthologUtils](https://datasnakes.github.io/OrthoEvolution/reference/utilities.OrthologUtils.html)
- [utilities.ManagerUtils](https://datasnakes.github.io/OrthoEvolution/reference/utilities.ManagerUtils.html)
- [utilities.CookieUtils](https://datasnakes.github.io/OrthoEvolution/reference/utilities.CookieUtils.html)
- [utilities.PackageVersion](https://datasnakes.github.io/OrthoEvolution/reference/utilities.PackageVersion.html)
- [utilities.FunctionRepeater](https://datasnakes.github.io/OrthoEvolution/reference/utilities.FunctionRepeater.html)
- [utilities.FullUtilities](https://datasnakes.github.io/OrthoEvolution/reference/utilities.FullUtilities.html)
- [OrthoEvolWarning](https://datasnakes.github.io/OrthoEvolution/reference/OrthoEvolWarning.html): This is the OrthoEvol main warning class
- [OrthoEvolDevelopmentWarning](https://datasnakes.github.io/OrthoEvolution/reference/OrthoEvolDevelopmentWarning.html): This is the OrthoEvol developmental code warning subclass
- [OrthoEvolDeprecationWarning](https://datasnakes.github.io/OrthoEvolution/reference/OrthoEvolDeprecationWarning.html): This is the Deprecation Warning subclass