Tools to work in phylogenomics, from NSG group http://nymphalidae.utu.fi
Project description
#PyPhyloGenomics 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](http://docs.python-requests.org/en/latest/user/install/). 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](http://www.parallelpython.com/content/view/15/30/) 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](http://biopython.org/wiki/Download). Or:
sudo apt-get install python-biopython
### BeatutifulSoup Download and install from [here](http://www.crummy.com/software/BeautifulSoup/). 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](http://www.drive5.com/muscle/downloads.htm).
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.
### BLAST Download and install the BLAST+ executables from the [NCBI website](http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download). Or try:
sudo apt-get install ncbi-blast+
### fastx-toolkit Download and install from [here](http://hannonlab.cshl.edu/fastx_toolkit/). Or:
sudo apt-get install fastx-toolkit
## Reading PyPhyloGenomics’ documentation: Read the online documentation here: [http://carlosp420.github.io/PyPhyloGenomics/](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 ???
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