This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
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Project Description

A package to work on Phylogenomics.

[[In development.]]

Developers

Installing PyPhyloGenomics

PyPhyloGenomics has been developed in Python v2.7. The installer of PyPhyloGenomics will try to download and install all its dependencies as well. To install PyPhyloGenomics use setup.py:

python setup.py build python setup.py install

If it fails you can install the dependencies manually:

Install dependencies:

requests:

The package requests from here. Or try:

sudo apt-get install python-requests

Parallel Python (pp):

If you are using Ubuntu Linux or related:

sudo apt-get install python-pp

Otherwise, download the source code and install pp:

unzip pp-1.6.4.zip cd pp-1.6.4 python setup.py install

BioPython:

Download and install from here. Or:

sudo apt-get install python-biopython

BeatutifulSoup

Download and install from here. Or:

sudo apt-get install python-bs4

MUSCLE

It is necessary that you install MUSCLE so that PyPhyloGenomics can use it to align sequences. Download and install from here.

If you are using Windows you can download the executable file muscle3.8.31_i86win32.exe and save it in your Python folder (C:27) as muscle.exe.

BLAST

Download and install the BLAST+ executables from the NCBI website. Or try:

sudo apt-get install ncbi-blast+

fastx-toolkit

Download and install from here. Or:

sudo apt-get install fastx-toolkit

Reading PyPhyloGenomics’ documentation:

Read the online documentation here: http://carlosp420.github.io/PyPhyloGenomics/

Or, after installling do the following:

cd doc make html

Then open the file _build/html/index.html in your web-browser.

Reproduce our analysis:

You can reproduce all the steps detailed in our [Getting started with PyPhylogenomics] guide. Just use the command line in the same folder as the Makefile and type make ???

Release History

Release History

0.3.12

This version

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0.3.11

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0.3.10

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0.3.9

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0.3.8

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0.3.7

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0.3.6

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0.3.5

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0.3.4

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0.3.3

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0.3.1

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0.3.0

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Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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0.2.0

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0.1.0

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
PyPhyloGenomics-0.3.12.tar.gz (269.8 kB) Copy SHA256 Checksum SHA256 Source Nov 14, 2013

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