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#PyPhyloGenomics A package to work on Phylogenomics.

##Developers

• Carlos Peña (email: [email protected])
• 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

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:\Python27) as muscle.exe.

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

sudo apt-get install ncbi-blast+

Download and install from here. Or:

sudo apt-get install fastx-toolkit

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.

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 ???