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Create and maintain phylogenetic "reference packages" of biological sequences.
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README.rst

TAXTASTIC

Installing

taxtastic requires Python 2.7. The simplest method of installing is using pip:

pip install taxtastic

If you don't have pip, try:

easy_install taxtastic

Either of these commands will install taxtastic along with required dependencies.

We love it, but what is it?

Taxtastic is software written in python used to build and maintain reference packages-- i.e. collections of reference trees, reference alignments, profiles, and associated taxonomic information.

A script named taxit provides a command line interface:

% ./taxit -h


usage: taxit [-h] [-V]

             {info,rollback,help,create,strip,taxids,new_database,check,reroot,refpkg_intersection,lonelynodes,update_taxids,rp,add_nodes,rollforward,update,findcompany,taxtable}
             ...

Creation, validation, and modification of reference packages for use with
`pplacer` and related software.

 positional arguments:
   {help,add_nodes,add_to_taxtable,check,composition,count_taxids,create,findcompany,info,lonelynodes,merge,new_database,refpkg_intersection,reroot,rollback,rollforward,rp,strip,taxids,taxtable,update,update_taxids}
     help                Detailed help for actions using `help <action>`
     add_nodes           Add new nodes to a database containing a taxonomy.
     add_to_taxtable     Add nodes to a taxtable
     check               Validate a reference package.
     composition         Show taxonomic composition of a reference package.
     count_taxids        Count tax_id appearances in a taxtable lineage
     create              Create a reference package
     findcompany         Find company for lonely nodes.
     info                Show information about reference packages.
     lonelynodes         Extracts tax ids of all lonely nodes in a taxtable.
     merge               Identify merged taxids and provide replacements.
     new_database        Download NCBI taxonomy and create a database
     refpkg_intersection
                         Find the intersection of a taxtable and a refpkg's
                         taxonomy.
     reroot              Taxonomically reroots a reference package
     rollback            Undo an operation performed on a refpkg.
     rollforward         Restore a change to a refpkg immediately after being
                         reverted.
     rp                  Resolve path; get the path to a file in the reference
                         package.
     strip               Remove rollback and rollforward information from a
                         refpkg
     taxids              Convert a list of taxonomic names into a list of
                         tax_ids
     taxtable            Create a tabular representation of taxonomic lineages
     update              Add or modify files or metadata in a refpkg
     update_taxids       Update obsolete tax_ids

optional arguments:
  -h, --help            show this help message and exit
  -V, --version         Print the version number and exit
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