tapir contains programs to estimate and plot phylogenetic informativeness for large datasets.
When using tapir, please cite:
- Faircloth BC, Chang J, Alfaro ME: TAPIR enables high throughput analysis of phylogenetic informativeness. arXiv:1202.1215
- Townsend JP: Profiling phylogenetic informativeness. Systematic Biol. 2007, 56:222-231.
- Pond SLK, Frost SDW, Muse SV: HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005, 21:676-679.
For examples of how people have used tapir for their own analyses, please see the wiki for links to manuscripts.
- hyphy2 (please download [osx or linux] or build a single-threaded hyphy2)
- Python 2.7
- numpy
- scipy
- dendropy
For ALL platforms, you must download a hyphy binary for your platform (osx or linux) and place that within your $PATH. To install the other dependencies (numpy, scipy), you may need to install a Fortran compiler on linux/osx, which is a dependency of numpy and scipy.
Install hyphy:
wget http://s3.faircloth-lab.org/packages/hyphy2.linux.gz gunzip hyphy2.*.gz chmod 0700 hyphy2.* mv hyphy2.* ~/Bin/hyphy2
On linux (ubuntu/debian), use:
apt-get install gfortran libatlas-base-dev liblapack-dev
Install tapir and dependencies, which include numpy and scipy (the reason we installed the dependencies above):
pip2 install https://github.com/faircloth-lab/tapir/archive/master.zip
To plot results, you will also need to:
apt-get install r-base r-base-dev pip2 install rpy2
Install hyphy:
wget http://s3.faircloth-lab.org/packages/hyphy2.osx.gz gunzip hyphy2.*.gz chmod 0700 hyphy2.* mv hyphy2.* ~/Bin/hyphy2
Install Python with Homebrew:
brew tap homebrew/science brew install python@2
Then try installing tapir with:
pip2 install https://github.com/faircloth-lab/tapir/archive/master.zip
You might need to install tapir's dependencies first:
brew install numpy scipy
To plot results, you need to install R and then install rpy2:
pip2 install rpy2
Download the source for hyphy from http://hyphy.org/w/index.php/Main_Page and compile a single-threaded version.
Install numpy, scipy, and dendropy for your platform. Alternatively, you can try:
pip2 install https://github.com/faircloth-lab/tapir/archive/master.zip
Which may install the necessary dependencies. Alternatively, install the dependencies manually, and then:
curl -L https://github.com/faircloth-lab/tapir/archive/master.zip | tar xzv cd tapir* python setup.py build python setup.py test python setup.py install
If you didn't run the tests using python setup.py test above, you can also:
import tapir tapir.test()
To run:
python tapir_compute.py Input_Folder_of_Nexus_Files/ Input.tree \
--output Output_Directory \
--intervals=32-42,88-98,95-105,164-174 \
--times=37,93,100,170 \
--multiprocessing
--multiprocessing is optional, without it, each locus will be run consecutively.
If you have already run the above and saved results to your output folder (see below), you can use the pre-existing site-rate records rather than estimating those again with:
python tapir_compute.py Input_Folder_of_Site_Rate_JSON_Files/ Input.tree \ --output Output_Directory \ --intervals=32-42,88-98,95-105,164-174 \ --times=37,93,100,170 \ --multiprocessing \ --site-rates
tapir writes results to a sqlite database in the output directory of your choosing. This directory also holds site rate files in JSON format for each locus passed through tapir_compute.py.
You can access the results in the database as follows. For more examples, including plotting, see the documentation
crank up sqlite:
sqlite3 Output_Directory/phylogenetic-informativeness.sqlite
get integral data for all epochs:
select locus, interval, pi from loci, interval where loci.id = interval.id
get integral data for a specific epoch:
select locus, interval, pi from loci, interval where interval = '95-105' and loci.id = interval.id;
get the count of loci having max(PI) at different epochs:
create temporary table max as select id, max(pi) as max from interval group by id; create temporary table t as select interval.id, interval, max from interval, max where interval.pi = max.max; select interval, count(*) from t group by interval;
tapir contains plotting scripts to help you plot data within a results database and compare data between different databases. tapir uses RPY and R to do this. You can also plot data directly in R. Until we finish the documentation, please see the wiki for examples.
Please use the issue tracker for help building and using tapir.
BCF thanks SP Hubbell, PA Gowaty, RT Brumfield, TC Glenn, NG Crawford, JE McCormack, and M Reasel. JC and MEA thank J Eastman and J Brown for thoughtful comments about PI. We thank Francesc Lopez-Giraldez and Jeffrey Townsend for providing us with a copy of their web-application source code and helpful discussion.