OrthoEvolution
User Guide
Reference
API
/
Orthologs.Phylogenetics.PhyML
API Index
Ortholog discovery
Orthologs.Blast.BaseComparativeGenetics
Orthologs.Blast.ComparativeGenetics
Orthologs.Blast.BaseBlastN
Orthologs.Blast.OrthoBlastN
Sequence retrieval
Orthologs.GenBank.GenBank
Tools.ftp.BaseFTPClient
Tools.ftp.NcbiFTPClient
Tools.mygene.MyGene
Alignment and phylogenetics
Orthologs.Align.ClustalO
Orthologs.Align.Guidance2Commandline
Orthologs.Align.Pal2NalCommandline
Orthologs.Align.MultipleSequenceAlignment
Orthologs.Phylogenetics.RelaxPhylip
Orthologs.Phylogenetics.ETE3PAML
Orthologs.Phylogenetics.PhyML
Orthologs.Phylogenetics.Phylip
Orthologs.Phylogenetics.IQTreeCommandline
Orthologs.Phylogenetics.FilteredTree
Orthologs.Phylogenetics.TreeViz
Orthologs.Phylogenetics.PAML.CodemlRun
Project and data management
Manager.management.Management
Manager.management.RepoManagement
Manager.management.UserManagement
Manager.management.WebsiteManagement
Manager.management.ProjectManagement
Manager.data_management.DataMana
Manager.database_management.BaseDatabaseManagement
Manager.database_management.DatabaseManagement
Manager.database_dispatcher.DatabaseDispatcher
Manager.biosql.biosql.BaseBioSQL
Manager.biosql.biosql.SQLiteBioSQL
Manager.biosql.biosql.MySQLBioSQL
Execution and supporting tools
Tools.pbs.BaseQsub
Tools.pbs.Qsub
Tools.pbs.BaseQstat
Tools.pbs.Qstat
Tools.pbs.MultiQstat
Tools.pbs.TargetJobKeyError
Tools.slurm.SlurmClient
Tools.slurm.SlurmJob
Tools.slurm.SlurmCommandNotFoundError
Tools.parallel.Multiprocess
Tools.logit.LogIt
Tools.pybasher.PyBasher
Tools.send2server.S2S
Tools.slackify.Slackify
Templates and utilities
Cookies.Oven
Cookies.CookBook
resources.package_resource_path
utilities.DuplicateAnalysis
utilities.BlastUtils
utilities.GenbankUtils
utilities.OrthologUtils
utilities.ManagerUtils
utilities.CookieUtils
utilities.PackageVersion
utilities.FunctionRepeater
utilities.FullUtilities
OrthoEvolWarning
OrthoEvolDevelopmentWarning
OrthoEvolDeprecationWarning
Orthologs.Phylogenetics.PhyML
Orthologs.Phylogenetics.PhyML
Usage
PhyML tools.