A package to work on Phylogenomics.
[[In development.]]
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 ???
1 maintainer
Metadata
1 maintainer
Release files for PyPhyloGenomics 0.3.12
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Release files / PyPhyloGenomics-0.3.12.tar.gz
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