Code for reproducing the HAL graph shown in Figure S7 of Cooke et al 2017 C++ dependencies: HAL: github.com/ComparativeGenomicsToolkit/hal sonLib: github.com/benedictpaten/sonLib Python dependencies: numpy: http://www.numpy.org scipy: https://www.scipy.org newick: https://pypi.python.org/pypi/newick R dependencies: ggplot2: http://ggplot2.org plyr: http://plyr.had.co.nz reshape2: https://github.com/hadley/reshape RColorBrewer: https://cran.r-project.org/web/packages/RColorBrewer/index.html IRanges: http://bioconductor.org/packages/release/bioc/html/IRanges.html ############################################################################################### Installation: Probably the easiest way to install the C++ dependencies is to install progressive cactus, which automatically installs them as submodules: git clone git://github.com/glennhickey/progressiveCactus.git cd progressiveCactus git pull git submodule update --init make Next, change the following line of make.sh to the path to your progressive cactus installation: PGPATH=<path to your progressive cactus installation> Fetch the code for intervaltree: git submodule init git submodule update Then, to compile haltraverse: ./make.sh To use haltraverse, be sure to add the following path to the environmental variable LD_LIBRARY_PATH: progressiveCactus/submodules/hdf5/lib/ ############################################################################################### Use: Align sequences with progressive cactus (Already done for you--see wga6.hal): runProgressiveCactus.sh wga6.txt wga6 wga6/wga6.hal --stats & Traverse HAL graph and print edges: haltraverse --bed wga6.bed --root Anc0 wga6.hal > wga6.edges Get unique set of edges: cat wga6.edges | sort | uniq > wga6.unique.edges cut -f 1-9 wga6.unique.edges | sort | uniq > wga6.no_features.edges Get the newick-formatted tree used in the PG alignment: halStats --tree wga6.hal > wga6.newick Find the optimal order and orientation of sequences for plotting: python count_inversions_greedy.py wga6.newick wga6.no_features.edges > wga6.config Plot the HAL graph by running the R code contained in the following file: halplot.r