PyPhyloGenomics 0.3.5

Tools to work in phylogenomics, from NSG group http://nymphalidae.utu.fi

Developers

• Carlos Peña (email: carlos.pena@utu.fi)
• Victor Solis
• Pavel Matos
• Chris Wheat

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 ???