competititiveRooting
comparing various rooting algorithms for phylogenetic language trees
To replicate my analysis, you need python3 to be installed. I assume the executable python to start python3. Also, an executable for RAxML (https://cme.h-its.org/exelixis/web/software/raxml/index.html) needs to be in your search path.
The file asjp/asjp18Clustered.csvwas obtained by applying the procedure described in Jäger, G., 2018. Global-scale phylogenetic linguistic inference from lexical resources, Scientific Data 5, 180189, 2018, doi.org/10.1038/sdata.2018.189. to the data from ASJP v. 18.
To install the required python packages:
pip install -r requirements.txt
To obtain the constraint tree from Glottolog:
wget https://cdstar.shh.mpg.de/bitstreams/EAEA0-9478-C22F-4AAF-0/tree_glottolog_newick.txt
To obtain the ASJP data:
cd asjp
wget https://cdstar.shh.mpg.de/bitstreams/EAEA0-E32A-2C2D-B777-0/asjp_dataset.cldf.zip
unzip asjp_dataset.cldf.zip
wget https://cdstar.shh.mpg.de/bitstreams/EAEA0-E32A-2C2D-B777-0/asjp_dataset.tab.zip
unzip unzip asjp_dataset.tab.zip
cd ..
You need to install the program tqDist:
wget http://users-cs.au.dk/cstorm/software/tqdist/files/tqDist-1.0.1.zip
unzip tqDist-1.0.1.zip
cd tqDist-1.0.1
Follow the "Build procedure" described in README. I got error messages when I ran "make", but adding the lines
#include <string.h>
#include <stdio.h>
to the headers of the files all_pairs_quartet_distance.cpp, pairs_triplet_distance.cpp, test_triplet.cpp, pairs_quartet_distance.cpp, quartet_dist.cpp, triplet_dist.cpp in the directory tqDist solved the problem.
cd ..
Finally, you need the script mad.py by the authors of Tria, F. D. K., Landan, G. and Dagan, T. Nat. Ecol. Evol. 1, 0193 (2017):
wget https://www.mikrobio.uni-kiel.de/de/ag-dagan/ressourcen/mad2-2.zip unzip mad2-2.zip
The actual analysis is carried out by the commands
python extractGlottologTree.py
python inferTrees.py
python madRooting.py
python outgroupRooting.py
python midpointRooting.py
python yuleRooting.py
python getTripletDistances.py