Metadata-Version: 2.1
Name: phylotypes
Version: 0.0.2
Summary: Group phylogenetically placed sequence variants into phylotypes
Home-page: https://github.com/jgolob/phylotypes
Author: Jonathan Louis Golob
Author-email: j-dev@golob.org
License: UNKNOWN
Project-URL: Bug Tracker, https://github.com/jgolob/phylotypes/issues
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE

# Phylotypes

Group features (e.g. 16s rRNA gene variable region sequence variants) placed on a common phylogenetic tree by phylogenetic distance.

This is particularly useful when attempting a metanalysis of 16s rRNA gene variable region amplicons, in which the amplicons were made with different primers, etc.

### Input:
`--jplace <file>` A jplace file (deduplicated) as made by [pplacer](https://matsen.fhcrc.org/pplacer/) or [epa-ng](https://github.com/Pbdas/epa-ng).

### Output:
`--out <file>` Path where the output should be placed in `CSV` format. This will be a header-containing CSV file in long-format with two columns: phylogroup and feature-id.

### Parameters:
`--lwr-overlap <0.0 - 1.0>` Minimum like-weight-ratio overlap for two placed features (e.g. sequence variants) to be pre-grouped. Default of 0.1 should be fine for most use cases.

`--threshold_pd <float>` Phylogenetic distance at which to cluster features. Default of 1.0 corresponds roughly to somewhere between species-level and genus-level grouping for 16s rRNA V4 region amplicons. 


