Hybrid-coal

Hybrid-coal is used to compute gene tree probabilities given species network under coalescent process. We use a new representation of the species network likelihood that expresses the probability distribution of the gene tree topolgies as a linear combination of gene tree distributions given a set of species trees.

Version	Branch	Travis CI Build Status	Circle CI Build Status
Development Version	dev

##NEWS

• 31-Oct-2016 Paper accepted by Systematic Biology.
• 24-Feb-2016 v0.2-beta
• 30-Aug-2015 v0.1-beta

##CITATION Sha Zhu and James H. Degnan Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent Syst Biol 2016 : syw097v1-syw097.

##DOCUMENTATION

##BEFORE INSTALLATION

To install hybrid-coal, first install the following packages and libraries

on Debian/Ubuntu based systems:

apt-get install git-core build-essential autoconf autoconf-archive libcppunit-dev graphviz

on Mac OS:

port install git cppunit automake autoconf autoconf-archive graphviz

DOWNLOAD AND COMPILE

Download and extract source code from

• tar.gz
• zip

or use git checkout, then type the following commands:

./bootstrap
make

##ASSUMPTION Input network files are written in extended newick format.

##LICENCE You can freely use all code in this project under the conditions of the GNU GPL Version 3 or later.

##HOW IT WORKS

Program parameters and options:

Options	Useage
-h or -help	Help. List the following content.

         -gt STR | Input the gene tree string string through command line or a file.
         -sp STR | Input the species network/tree string through command line or a file.
          -gtopo | To generate the gene tree topologies of a given set of taxa.

-plot/-dot [option] | Use LaTEX(-plot) or Dot (-dot) to draw the input (defined by -spcu) network(tree). [-branch] | Branch lengths will be labelled in the figure. -o STR | Specify the file name prefix of the output.

##Examples:

hybrid-coal -sp '((((B:1,C:1)s1:1)h1#.5:1,A:3)s2:1,(h1#.5:1,D:3)s3:1)r;'
hybrid-coal -sp trees/4_tax_sp_nt1_para -gt '(((A,D),C),B);'
hybrid-coal -sp trees/4_tax_sp_nt1_para -plot
hybrid-coal -sp trees/4_tax_sp_nt1_para -plot -branch
hybrid-coal -sp trees/4_tax_sp_nt1_para -plot -label
hybrid-coal -sp trees/4_tax_sp_nt1_para -dot
hybrid-coal -sp trees/4_tax_sp_nt1_para -gtopo