Continual gene tree updating. Uses a tree from Open tree of Life (or your own tree) and an alignment to search for and adds homologous sequences to phylogenetic inference.
The tool is under current development in the McTavish Lab. Please contact ejmctavish, gmail if you need any help!
see also here
Dependencies (need to be in path):
- PaPaRa http://sco.h-its.org/exelixis/web/software/papara/index.html
- Raxml http://sco.h-its.org/exelixis/web/software/raxml/index.html
- BLAST+ https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
These will all be installed if you install physcraper using python setup.py install
(but note, if you are using virtualenv there are some weird interactions with setuptools and python 2.7.6)
- Dendropy https://pythonhosted.org/DendroPy/
- Peyotl https://github.com/OpenTreeOfLife/peyotl (currently needs to be on physcraper branch)
- Biopython http://biopython.org/wiki/Download
The tool uses several databases, which can automatically be downloaded/updated from ncbi. If the tool wants to access the site, you will be asked for input (yes or no), as the tool will then access ncbi, which is a US government website!
For a description of which settings need to be changed and how to set-up a run, see here.
Example runs and datasets
There is a full example python script with comments in
Some more example files can be found in
If you want to try running physcraper use the testdata which is in
More information will follow soon.
The Documentation about the different classes can be found here.
There are some tests here and here, which test the major functionality of the code. If you want to test if the code works on your machine, please run
python tests/testfilesetup.py and then