Skip to main content

Python API that provides simple tools for doing phylogenetics.

Project description

Python API with tools for doing phylogenetics

This is the master repository for the `phylogenetics` Python package. This package includes a lightweight, simple-to-use API for managing and processing phylogenetic data. Many of the modules included in this package originated from Dr. [Mike Harms']( `phylo_tools` and have been converted to API's. Read the Wiki to learn more about the internal structure.

The foundation of this API are the `Homolog` and `HomologSet` objects. These objects offer a simple datastructure that manages the metadata for a set of sequences in a phylogenetics/reconstruction project. These objects are easily queried, updated, and saved into many formats (i.e. fasta, csv, phylip, pickle, and json).

An metadata inside a homolog (__dict__ attribute) might look might look like this:

>>> print(homolog.__dict__)

"id" : "XX00000000",
"species" : "S100A5",
"organism" : "human",
"length" : 180,
"latest_align" : "----ASK---F-AFELG--SKA---DGKASEK-A---...",
"align_1" : "--------------ASK-------F-AFELG-----SKA--DFLASEK--A--...",


>>> homolog.fasta()


>>> homolog.write("homolog.fasta", format="fasta") # writes to file "homolog.fasta"


Clone this repo locally:

git clone

Navigate to this directory, and install this python package with

python install

**NOTE:** Many of modules in this API require

Setting up for Development

Git must be installed to clone and contribute to this project

1. Fork this repository on Github
2. Clone that repository locally
git clone
3. Navigate to this directory, and install (softly) this python package with
cd phylogenetics
python develop
4. Add another remote link to the master version, call it `upstream`.
git remote add upstream
5. Start a branch locally from local master
git checkout -B <branch-name>
6. Make changes and commit to that branch.
git commit -a -m "<commit message>"
7. Push to your fork on github (which you called `upstream`).
git push upstream <branch-name>
8. Pull request the branch on Github into this master repository on Github.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for phylogenetics, version 0.1
Filename, size File type Python version Upload date Hashes
Filename, size phylogenetics-0.1-py3-none-any.whl (16.6 kB) File type Wheel Python version 3.4 Upload date Hashes View
Filename, size phylogenetics-0.1.tar.gz (12.0 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page