Metadata-Version: 2.1
Name: tanos
Version: 0.0.1b6
Summary: TANOS: TAxon jackknife for NOdal Stability. In phylogenetic trees, calculate how resilient nodes are to the removal of taxa
Home-page: https://github.com/pickettbd/tanos
Author: Brandon Pickett
Author-email: pickettbd@byu.edu
License: UNKNOWN
Project-URL: Source, https://github.com/pickettbd/tanos
Project-URL: Bug Reports, https://github.com/pickettbd/tanos/issues
Project-URL: Buy me a soda!, http://buymeacoff.ee/pickettbd
Description: # TANOS: TAxon jackknife for NOdal Stability
        
        ## Table of Contents
           [I. Introduction](#i-introduction)<br>
          [II. Installation Instructions](#ii-installation-instructions)<br>
         [III. Usage Instructions](#iii-usage-instructions)<br>
          [IV. License](#iv-license)<br>
          [V. Contributors](#v-contributors)<br>
         [VI. Citation](#vi-citation)<br>
        [VII. Contact](#vii-contact)
        
        
        ## I. Introduction
        In phylogenetic trees, assessing the stability of a node is paramount to having
        confidence in the quality of the topology. Several strategies exist to evaluate
        a node, with bootstrap support being particularly popular. Most methods rely on
        how consistently characters from the input data matrix are in a given state to
        judge the node. We seek to evaluate the stability of the node by determining how
        resilient nodes are to the removal of taxa. This package can calculate the taxa
        resiliency for a provided tree. To determine this, one must remove a taxon from
        the alignment (jackknife sampling) and build a new tree, comparing it to the
        original tree. To avoid anomalies, a new tree must be built multiple times (say
        50). This process must be repeated for each taxon. Thus, if 100 taxa are in a
        given tree and 50 replicates are performed for the removal of each taxon then
        5,000 new trees are built. These new trees can be provided with the original tree
        to our package for comparison to determine how frequently different clades appear.
        The intent is to assign a value to each node, similar to bootstrapping. A value
        of 1 indicates 100% of sampled trees includes the grouping in that clade (sans
        the one taxon intentionally removed). Valid values fit in the range [0,1]. Note
        that this value has no meaning for leaf nodes, parents of leaf nodes, and the
        root node.
        
        Please note that this package assumes the following has already been performed:
        
        1. The original alignment of all taxa
        2. A tree built with all taxa
        3. "jackknifing" the alignment (making one copy per taxon in the tree, minus that taxon)
        4. New trees built using the "jackknifed" alignments with a pre-determined level of replication
        
        Assuming the interested user of this package wishes to generate nodal stability
        scores for a tree, steps #1-2 will already be completed. Step #3 is trivially
        accomplished with basic scripting. See the scripts directory of the repository
        for an example. Step #4 is conceptually simple, but more difficult to manage as
        the number of taxa and/or replicates increases. An example script to manage such
        a task on a computing cluster under [SLURM](https://slurm.schedmd.com) control
        using [IQ-TREE](http://www.iqtree.org) is also provided. Note that these are
        simply example scripts, not fully-tested programs; modifications will be required
        for your system and situation, especially if you intend to use an alternate
        directory structure, tree inference software, or grid control engine. Please note
        that if you installed tanos with pip, you will not see these scripts as they are
        not included in the PyPI manifest; you will need to download the repo from GitHub
        to have access to them. Please see the
        [README](https://github.com/pickettbd/tanos/blob/master/scripts/README.md) file
        in the scripts directory for additional details.
        
        This program must have access to all the relevant trees (_i.e._, the original/main
        tree and the "jackknifed" trees) and a mapping of which trees are associated
        with which taxa. A default directory structure and file naming scheme is assumed.
        These assumptions can be modified to some degree, or bypassed entirely, with
        certain command-line arguments. Please consult the section [III. Usage
        Instructions](#iii-usage-instructions) for details.
        
        We are in the process of publishing a paper describing this work. Once
        available, we will provide relevant details here:
        
        See our paper in [_journal_](#readme) for further information:<br>
        <span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>[https://sub-domain.domain.tld/some/path/to/resource](#readme)
        
        
        ## II. Installation Instructions
        This package is written in [Python](https://www.python.org). You must have a version of Python (v3.6+) that supports [f-strings](https://docs.python.org/3/reference/lexical_analysis.html#f-strings). This package also depends on the following Python modules: sys, re, pkgutil, argparse, and pathlib, which are all included by default in most Python installations. Installation may be accomplished using pip like this:
        
        <span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>`pip install tanos`
        
        Alternately, you may install it manually using setuptools like this:
        
        <span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</span>`python setup.py install`
        
        If running `setup.py`, you may wish to add `--user` or `--prefix` for an
        installation in non-default locations.
        
        ## III. Usage Instructions
        Please run `tanos -h` or `tanos --help`.
        
        
        ## IV. License
        Please see the [LICENSE](https://github.com/pickettbd/tanos/blob/master/LICENSE).
        
        
        ## V. Contributors
        Brandon Pickett (Github: [@pickettbd](https://github.com/pickettbd)) is the sole author of this software.
        
        
        ## VI. Citation
        Until a version of the paper is available, we ask that you cite the Github
        repository. Thereafter, you will be able to include a citation following
        this general form:
        
        > Powell GS, Pickett BD, Martin GJ, Whiting MF, Ridge PG, Bybee SM. Paper title. _journal_. Year. Volume(Issue):pages.
        
        
        ## VII. Contact
        For questions, comments, concerns, etc., please open an issue on Github.
        
        **Note:** Before asking for help, please ensure you (a) are using the latest
        official release and (b) consult first the section [III. Usage Instructions](#iii-usage-instructions).
        
        
Keywords: phylogeny,phylogenetic,taxonomy,taxa,taxon,resilience,resiliency,tree,systematics,nodal stability
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Environment :: Console
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Requires-Python: >=3.6, <4
Description-Content-Type: text/markdown
