Metadata-Version: 2.1
Name: treesapp
Version: 0.6.8
Summary: TreeSAPP is a functional and taxonomic annotation tool for genomes and metagenomes.
Home-page: https://github.com/hallamlab/TreeSAPP
Author: Connor Morgan-Lang
Author-email: c.morganlang@gmail.com
License: GPL-3.0
Platform: UNKNOWN
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: C++
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
Requires-Dist: samsum (>=0.1.0)
Requires-Dist: pygtrie (>=2.3)
Requires-Dist: ete3 (>=3.1.1)
Requires-Dist: numpy (>=1.18.1)
Requires-Dist: biopython (>=1.68)
Requires-Dist: scipy
Requires-Dist: six (>=1.14.0)

# TreeSAPP: Tree-based Sensitive and Accurate Phylogenetic Profiler

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## Overview

TreeSAPP is a python package for phylogenetically annotating proteins from genomes and metagenomes.

## Quick start

We recommend installing TreeSAPP into it's own conda environment with the following command:

```bash
conda create -n treesapp_cenv -c bioconda -c conda-forge treesapp
conda activate treesapp_cenv
```

For more options please visit the wiki page on [Installing TreeSAPP](https://github.com/hallamlab/TreeSAPP/wiki/Installing-TreeSAPP).

To list all the sub-commands run `treesapp`.

To test the `assign` workflow, run:
```bash
treesapp assign -i TreeSAPP/test_data/marker_test_suite.faa -m prot --trim_align -o assign_test -t M0701,M0702,M0705
```

To classify sequences in your genome of interest:
```bash
treesapp assign -i my.fasta -o ~/path/to/output/directory/
```

## Tutorials

If we do not yet have a reference package for a gene you are interested in,
please try [building a new reference package](https://github.com/hallamlab/TreeSAPP/wiki/Building-reference-packages-with-TreeSAPP).
Of course, if you run into any problems or would like to collaborate on building many reference packages
don't hesitate to email us or create a new issue with an 'enhancement' label.

To determine whether the sequences used to build your new reference package are what you think they are,
 and whether it might unexpectedly annotate homologous sequences,
 see the [purity tutorial](https://github.com/hallamlab/TreeSAPP/wiki/Testing-the-functional-purity-of-reference-packages).

If you are working with a particularly complex reference package, from an orthologous group for example, or have extra
 phylogenetic information you'd like to include in your classifications,
 try [annotating extra features](https://github.com/hallamlab/TreeSAPP/wiki/Layering-annotations-onto-classifications) with `treesapp layer`.

### Yet to come
-   [Interpreting `treesapp assign` results]()
-   [Evaluating classification accuracy]()
-   [Taxonomically decorating trees for iTOL]()
-   [Terraform](https://github.com/hallamlab/TreeSAPP/wiki/Running-TreeSAPP-on-Google-Cloud-Platform)

## Authors

* Connor Morgan-Lang ([cmorganl](https://github.com/cmorganl), maintainer)
* Ryan McLaughlin ([McGlock](https://github.com/McGlock))
* Grace Zhang ([grace72](https://github.com/gracez72))
* Kevin Chan ([kevinxchan](https://github.com/kevinxchan))
* Zachary Armstrong
* Steven J. Hallam



