merge conflict

.gitignore

@@ -94,3 +94,5 @@ compile
 *gcov
 *gcno
 *gcda
+compile
+test-driver

.travis.yml

@@ -9,7 +9,7 @@ compiler:
 before_install:
   - echo $LANG
   - echo $LC_ALL
-  - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get update -qq; sudo apt-get install -qq git-core libcppunit-dev graphviz valgrind r-base-core; fi
+  - if [ $TRAVIS_OS_NAME == linux ]; then sudo apt-get update -qq; sudo apt-get install -qq git-core libcppunit-dev graphviz valgrind r-base-core texlive-latex-extra doxygen; fi
   - if [ $TRAVIS_OS_NAME == osx ]; then rvm get 1.29.3; brew update; brew doctor; rvm install 2.3.3; fi
   - if [ $TRAVIS_OS_NAME == osx ]; then brew update ; fi
   - if [ $TRAVIS_OS_NAME == osx ]; then brew install llvm cppunit zlib ; fi

Makefile.am

@@ -1,5 +1,5 @@
-EXTRA_DIST = trees/*tax* bootstrap example/eg* src/Makefile version src/boost src/checkfiles.sh
-
+SUBDIRS = doc
+EXTRA_DIST = Doxyfile trees/*tax* src/Makefile version src/boost src/checkfiles.sh bootstrap example/eg* doc/*.pdf doc/*.tex doc/manual.bbl doc/manual.blg 
 #DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 distdir = $(PACKAGE)-$(VERSION)
 

README.md

@@ -32,11 +32,11 @@ To install hybrid-Lambda, first install the following packages and libraries
 
 on Debian/Ubuntu based systems:
 ```bash
-apt-get install git-core build-essential autoconf autoconf-archive libcppunit-dev graphviz 
+apt-get install build-essential autoconf autoconf-archive libcppunit-dev libboost-all-dev doxygen graphviz
 ```
 on Mac OS:
 ```bash
-port install git cppunit automake autoconf autoconf-archive graphviz
+port install automake autoconf autoconf-archive cppunit boost doxygen graphviz
 ```
 
 then type the following commands:

configure.ac

@@ -10,6 +10,9 @@ AM_INIT_AUTOMAKE([1.9 tar-ustar subdir-objects])
 m4_ifndef([AM_SILENT_RULES], [m4_define([AM_SILENT_RULES],[])])
 AM_SILENT_RULES([yes])
 
+# Load macros in 'm4'-dir
+AC_CONFIG_MACRO_DIR([m4])
+
 AC_CANONICAL_HOST
 
 # Checks for programs.
@@ -35,8 +38,28 @@ AC_FUNC_REALLOC
 
 #AC_CHECK_FUNCS([floor])
 #AC_CHECK_FUNCS([pow])
-AC_HEADER_STDBOOL
+#AC_HEADER_STDBOOL
+
+m4_include([m4/ac_doxygen.m4])
+DX_INIT_DOXYGEN(hybrid-Lambda, Doxyfile, html/)
+DX_HTML_FEATURE(ON)
+DX_CHM_FEATURE(OFF)
+DX_CHI_FEATURE(OFF)
+DX_MAN_FEATURE(OFF)
+DX_RTF_FEATURE(OFF)
+DX_XML_FEATURE(OFF)
+DX_PDF_FEATURE(OFF)
+DX_PS_FEATURE(OFF)
+
+
+AC_CHECK_PROG(PDFLATEX, pdflatex, pdflatex)
+AC_CHECK_PROG(BIBTEX, bibtex,bibtex)
+if test -z "$PDFLATEX"; then
+  AC_MSG_WARN([Unable to create PDF version of the user manual.])
+fi
+
+AM_CONDITIONAL([HAVE_PDFLATEX], test -n "$PDFLATEX")
 
-AC_CONFIG_FILES([Makefile])
+AC_CONFIG_FILES([Makefile doc/Makefile])
 AC_OUTPUT
 

doc/Makefile.am

@@ -0,0 +1,32 @@
+#docfiles = manual.tex 
+if HAVE_PDFLATEX
+doc_DATA = manual.pdf
+MANNAME = manual
+MANTEXSRC = $(MANNAME).tex
+MANAUX = $(MANNAME).aux
+MANPDF = $(MANNAME).pdf
+DOCDIR=$(abs_top_builddir)/doc
+CLEANFILES = $(MANPDF) $(MANNAME).log $(MANNAME).idx $(MANNAME).out \
+ $(MANNAME).toc $(MANAUX) 
+#$(MANNAME).bbl $(MANNAME).blg 
+
+$(MANPDF): $(srcdir)/$(MANTEXSRC)
+	$(PDFLATEX) $(MANTEXSRC)
+#	$(BIBTEX) $(MANAUX)
+#	$(PDFLATEX) $(MANTEXSRC)
+	$(PDFLATEX) $(MANTEXSRC)
+endif
+#dist_doc_DATA = $(docfiles)
+
+EXTRA_DIST = manual.pdf 
+
+#SUBDIRS =
+
+net1fig: 
+	rm net1-figure*
+	latex --shell-escape net1.tex
+	convert -density 300 net1-figure0.eps -resize 1024x1024 net1-figure0.png
+	convert -density 300 net1-figure1.eps -resize 1024x1024 net1-figure1.png
+	convert -density 300 net1-figure2.eps -resize 1024x1024 net1-figure2.png
+
+#if [ -a net1-figure0.md5 ] ; then rm net1-figure0.md5 ; fi

doc/hybridlambda_logo.tex

@@ -0,0 +1,59 @@
+\documentclass{article}
+\usepackage{tikz}
+\begin{document}
+
+\begin{tikzpicture}[ultra thick]
+\ifx\du\undefined
+  \newlength{\du}
+  \fi
+  \setlength{\du}{.8\unitlength}
+% \ifx\du\undefined
+%   \newlength{\du}
+%   \fi
+%   \setlength{\du}{2.5\unitlength}
+ \draw[help lines,step=10\du] (-55\du,0\du) grid (40\du,100\du);
+\draw(-55\du,0\du)--(-35\du,0\du);
+\draw(-20\du,0\du)--(-10\du,0\du);
+\draw(-10\du,0\du)--(-5\du,15\du);
+\draw(-20\du,0\du)--(-15\du,15\du);
+\draw(-15\du,15\du)--(-11\du,21.5\du);
+\draw(-11\du,21.5\du)--(-15\du,25\du);
+\draw(-35\du,0\du)--(-15\du,25\du);
+% \draw(-55\du,0\du)--(-20\du,45\du);
+\draw(-55\du,0\du)--(-35\du,25\du)--(-25\du,45\du)--(-20\du,85\du)--(-20\du,105\du);
+% \draw(-10\du,50\du)--(-10\du,45\du);
+%%%% square in the middle
+\draw(0\du,27.5\du)--(10\du,50\du);
+\draw(0\du,27.5\du)--(-10\du,42.5\du);
+\draw(-5\du,70\du)--(-10\du,42.5\du);
+\draw(-5\du,70\du)--(10\du,50\du);
+%%%% square in the middle
+\draw(45\du,0\du)--(30\du,0\du);
+\draw(15\du,0\du)--(0\du,0\du);
+\draw(0\du,0\du)--(-5\du,15\du);
+\draw(15\du,0\du)--(10\du,15\du);
+\draw(10\du,20\du)--(10\du,15\du);
+\draw(10\du,20\du)--(14\du,30\du);
+\draw(30\du,0\du)--(14\du,30\du);
+% \draw(45\du,0\du)--(10\du,45\du);
+\draw(45\du,0\du)--(30\du,30\du)--(25\du,50\du)--(5\du,85\du)--(5\du,105\du);
+% \draw(10\du,50\du)--(10\du,45\du);
+\draw[thick](-50\du,0\du)--(-49\du,1\du)--(-48\du,2\du)--(-45\du,3\du)--(-44\du,4\du)--(-45\du,5\du)--(-44\du,6\du)--(-41\du,7\du)--(-40\du,8\du)--(-39\du,9\du)--(-39\du,10\du);
+\draw[thick](-40\du,0\du)--(-39\du,1\du)--(-39\du,2\du)--(-39\du,3\du)--(-38\du,4\du)--(-40\du,5\du)--(-40\du,6\du)--(-39\du,7\du)--(-39\du,8\du)--(-39\du,9\du)--(-39\du,10\du);
+\draw[thick](-15\du,0\du)--(-15\du,1\du)--(-15\du,3\du)--(-14\du,4\du)--(-14\du,5\du)--(-13\du,7\du)--(-11\du,9\du)--(-11\du,10\du)--(-11\du,11\du)--(-12\du,12\du)--(-11\du,13\du)--(-11\du,14\du)--(-10\du,15\du);
+\draw[thick](5\du,0\du)--(5\du,1\du)--(5\du,2\du)--(3\du,5\du)--(3\du,6\du)--(2\du,7\du)--(3\du,8\du)--(2\du,10\du)--(1\du,11\du)--(2\du,12\du)--(1\du,13\du)--(1\du,14\du)--(0\du,15\du);
+%\draw[thick](10\du,0\du)--(10\du,1\du)--(8\du,4\du)--(7\du,5\du)--(8\du,6\du)--(8\du,7\du)--(7\du,8\du)--(7\du,10\du)--(6\du,13\du)--(5\du,14\du)--(5\du,15\du)--(5\du,17\du)--(5\du,19\du)--(7\du,21\du)--(6\du,23\du)--(6\du,25\du)--(7\du,27\du)--(7\du,29\du)--(8\du,31\du)--(8\du,33\du)--(10\du,35\du)--(10\du,37\du)--(10\du,40\du);
+\draw[thick](35\du,0\du)--(34\du,2\du)--(33\du,4\du)--(32\du,6\du)--(31\du,8\du)--(30\du,10\du)--(30\du,12\du)--(29\du,14\du)--(27\du,16\du)--(26\du,18\du)--(26\du,20\du)--(24\du,22\du)--(23\du,24\du)--(23\du,26\du)--(22\du,28\du)--(20\du,30\du);
+\draw[thick](-39\du,10\du)--(-38\du,12\du)--(-36\du,14\du)--(-36\du,16\du)--(-35\du,18\du)--(-32\du,20\du)--(-32\du,22\du)--(-31\du,24\du)--(-30\du,26\du)--(-29\du,28\du)--(-28\du,30\du)--(-25\du,32\du)--(-24\du,34\du)--(-23\du,36\du)--(-23\du,38\du)--(-22\du,40\du)--(-20\du,42\du)--(-18\du,44\du)--(-18\du,46\du)--(-17\du,48\du)--(-15\du,50\du);
+\draw[thick](-15\du,50\du)--(-15\du,51\du)--(-14\du,52\du)--(-14\du,53\du)--(-15\du,54\du)--(-13\du,55\du)--(-14\du,60\du)--(-14\du,64\du)--(-12\du,67\du)--(-9\du,69\du)--(-7\du,80\du); %left child of the root
+\draw[thick](20\du,40\du)--(19\du,42\du)--(16\du,44\du)--(15\du,46\du)--(14\du,48\du)--(13\du,50\du)--(12\du,52\du)--(11\du,54\du)--(5\du,56\du)--(5\du,58\du)--(-7\du,80\du); %right child of the root
+\draw[thick](20\du,30\du)--(19\du,31\du)--(18\du,32\du)--(17\du,33\du)--(15\du,34\du)--(15\du,35\du)--(14\du,36\du)--(12\du,37\du)--(13\du,38\du)--(10\du,39\du)--(10\du,40\du); %very right
+\draw[thick](-10\du,15\du)--(-8\du,16\du)--(-6\du,17\du)--(-4\du,18\du)--(-2\du,19\du)--(0\du,20\du);
+\draw[thick](0\du,20\du)--(2\du,24\du)--(3\du,26\du)--(4\du,28\du)--(5\du,30\du)--(6\du,32\du)--(8\du,34\du)--(7\du,36\du)--(10\du,38\du)--(10\du,40\du);
+\draw[thick](0\du,15\du)--(-2\du,18\du)--(-5\du,19\du)--(-5\du,20\du)--(-7\du,21\du)--(-6\du,22\du)--(-8\du,23\du)--(-9\du,24\du)--(-10\du,25\du)--(-12\du,26\du)--(-12\du,27\du)--(-14\du,28\du)--(-15\du,29\du)--(-15\du,30\du);
+\draw[thick](-15\du,30\du)--(-17\du,35\du)--(-16\du,40\du)--(-14\du,45\du)--(-15\du,50\du);
+
+% \pgfmathsetmacro{\Xb}{random(7)};
+%\draw[thick](-40\du,0\du)--(-39\du,1\du)--(-39\du,2\du)--(-39\du,3\du)--(-38\du,4\du)--(-40\du,5\du)--(-40\du,6\du)--(-39\du,7\du)--(-39\du,8\du)--(-39\du,9\du)--(-39\du,10\du);
+\end{tikzpicture}
+\end{document}

doc/manual.bbl

@@ -0,0 +1,53 @@
+\begin{thebibliography}{1}
+
+\bibitem{Cardona12008}
+Gabriel. Cardona, Francesc. Rossell, and Gabriel. Valiente.
+\newblock Extended {N}ewick: it is time for a standard representation of
+  phylogenetic networks.
+\newblock {\em BMC Bioinformatics}, 9(532-540), 2008.
+
+\bibitem{Eldon2012}
+Bjarki Eldon and James~H. Degnan.
+\newblock Multiple merger gene genealogies in two species: monophyly,
+  paraphyly, and polyphyly for two examples of {L}ambda coalescents.
+\newblock {\em Theoretical Population Biology}, 82:117--130, 2012.
+
+\bibitem{Eldon2006}
+Bjarki Eldon and John Wakeley.
+\newblock Coalescent processes when the distribution of offspring number among
+  individuals is highly skewed.
+\newblock {\em Genetics}, 172:2621--2633, 2006.
+
+\bibitem{Huson2010}
+D.H. Huson, R.~Rupp, and C.~Scornavacca.
+\newblock {\em Phylogenetic Networks: Concepts, Algorithms and Applications}.
+\newblock Cambridge University Press, Cambridge, UK, 2010.
+
+\bibitem{Matsumoto1998}
+M.~Matsumoto and T.~Nishimura.
+\newblock {Mersenne Twister}: A 623-dimensionally equidistributed uniform
+  {Pseudo-Random} number generator.
+\newblock {\em ACM Transactions on Modeling and Computer Simulation},
+  8(1):3--30, 1998.
+
+\bibitem{Olsen1990}
+Gary Olsen.
+\newblock {Gary Olsen's} interpretation of the ``{N}ewick's 8:45'' tree format
+  standard, 1990.
+\newblock http://evolution.genetics.washington.edu/phylip/newick\_doc.html. Feb
+  21, 2013.
+
+\bibitem{Rosenberg2003}
+Noah~A. Rosenberg.
+\newblock The shapes of neutral gene genealogies in two species: probabilities
+  of monophyly, paraphyly and polyphyly in a coalescent model.
+\newblock {\em Evolution}, 57(7):1465--1477, 2003.
+
+\bibitem{Schweinsberg2003}
+Jason Schweinsberg.
+\newblock Coalescent processes obtained from supercritical {G}alton--{W}atson
+  processes.
+\newblock {\em Stochastic Processes and their Applications}, 106:107--139,
+  2003.
+
+\end{thebibliography}

doc/manual.tex

@@ -0,0 +1,39 @@
+\documentclass[12pt]{article}
+ \usepackage{fullpage}
+\usepackage{graphics,graphicx,subfig}
+\usepackage{amsmath,multicol,lscape,framed,amssymb}
+\usepackage{graphicx,epic,subfig,graphicx,tikz,pifont}
+%\usepackage{multirow,epic}
+% \usepackage{algorithmic,algorithm}
+\usepackage{hyperref,hypcap}
+\usepackage{natbib}%
+\usepackage{longtable}
+\usepackage{textcomp}%to use \textquotesingle
+% \captionsetup{type=figure}
+\hypersetup{
+colorlinks,%
+citecolor=blue,%
+filecolor=black,%
+linkcolor=blue,%
+urlcolor=blue,
+}
+\usepackage{setspace}
+\bibliographystyle{plain}
+
+\bibstyle{plain}
+\newcommand{\HRule}{\noindent\rule{\linewidth}{1.5pt}}
+\newtheorem{alg}{Algorithm}
+\newcommand{\cm}[1]{\begin{center}{\tt #1}\end{center}}
+\newcommand{\hs}{{\tt hybrid-Lambda}}
+\begin{document}
+
+\title{Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees}
+\author{Sha (Joe) Zhu}
+\date{}
+\maketitle
+\input{sim_manual.tex}
+
+\bibliography{manual.bbl}
+
+\end{document}
+

doc/multi_in_net_tikz_fig.tex

@@ -0,0 +1,95 @@
+
+\begin{tikzpicture}[ultra thick]
+\ifx\du\undefined
+  \newlength{\du}
+  \fi
+  \setlength{\du}{2\unitlength}
+% \ifx\du\undefined
+%   \newlength{\du}
+%   \fi
+%   \setlength{\du}{2.5\unitlength}
+% \draw[help lines,step=5\du] (-55\du,0\du) grid (40\du,70\du);
+\draw(-55\du,0\du)--(-35\du,0\du);
+\draw(-20\du,0\du)--(-10\du,0\du);
+\draw(-10\du,0\du)--(-5\du,15\du);
+\draw(-20\du,0\du)--(-15\du,15\du);
+\draw(-15\du,15\du)--(-11\du,21.5\du);
+\draw(-11\du,21.5\du)--(-15\du,25\du);
+\draw(-35\du,0\du)--(-15\du,25\du);
+% \draw(-55\du,0\du)--(-20\du,45\du);
+\draw(-55\du,0\du)--(-35\du,25\du)--(-25\du,45\du)--(-20\du,50\du)--(-20\du,65\du);
+% \draw(-10\du,50\du)--(-10\du,45\du);
+\draw(0\du,22.5\du)--(-10\du,32.5\du);
+\draw(-5\du,45\du)--(-10\du,32.5\du);
+\draw(40\du,0\du)--(30\du,0\du);
+\draw(15\du,0\du)--(0\du,0\du);
+\draw(0\du,0\du)--(-5\du,15\du);
+\draw(15\du,0\du)--(10\du,15\du);
+\draw(10\du,20\du)--(10\du,15\du);
+\draw(10\du,20\du)--(14\du,30\du);
+\draw(30\du,0\du)--(14\du,30\du);
+% \draw(45\du,0\du)--(10\du,45\du);
+\draw(40\du,0\du)--(25\du,30\du)--(5\du,50\du)--(5\du,65\du);
+% \draw(10\du,50\du)--(10\du,45\du);
+\draw(0\du,22.5\du)--(5\du,35\du);
+\draw(-5\du,45\du)--(5\du,35\du);
+% \pgfmathsetmacro{\Xb}{random(7)};
+\fill(-39\du,10\du)[black]circle(2.5pt);
+\fill(-15\du,50\du)[black]circle(2.5pt);
+\fill(-5\du,60\du)[black]circle(2.5pt);
+\fill(10\du,40\du)[black]circle(2.5pt);
+\node at (-45\du,-5\du)[below]{\bf A};
+\node at (-15\du,-5\du)[below]{\bf B};
+\node at (7.5\du,-5\du)[below]{\bf C};
+\node at (35\du,-5\du)[below]{\bf D};
+\node at (-50\du,-7\du)[above]{\small a$_1$};
+\node at (-45\du,-7\du)[above]{\small a$_2$};
+\node at (-40\du,-7\du)[above]{\small a$_3$};
+\node at (-15\du,-7\du)[above]{\small b$_1$};
+\node at (5\du,-7\du)[above]{\small c$_1$};
+\node at (10\du,-7\du)[above]{\small c$_2$};
+\node at (35\du,-7\du)[above]{\small d$_1$};
+% \draw[thick](-39\du,10\du)--(-15\du,50\du);
+% \draw[thick](-15\du,50\du)--(-5\du,60\du);
+% \draw[thick](10\du,40\du)--(-5\du,60\du);
+% \draw[thick](35\du,0\du)--(20\du,30\du);
+% \draw[thick](20\du,30\du)--(10\du,40\du);
+% \draw[thick](-15\du,0\du)--(-10\du,15\du);
+% \draw[thick](-10\du,15\du)--(0\du,20\du);
+% \draw[thick](0\du,20\du)--(10\du,40\du);
+% \draw[thick](5\du,0\du)--(0\du,15\du);
+% \draw[thick](10\du,0\du)--(5\du,15\du);
+% \draw[thick](0\du,15\du)--(-15\du,30\du);
+% \draw[thick](-15\du,30\du)--(-15\du,50\du);
+% \draw[thick](5\du,15\du)--(10\du,40\du);
+\draw[thick](-40\du,0\du)--(-39\du,1\du)--(-39\du,2\du)--(-39\du,3\du)--(-38\du,4\du)--(-40\du,5\du)--(-40\du,6\du)--(-39\du,7\du)--(-39\du,8\du)--(-39\du,9\du)--(-39\du,10\du);
+\draw[thick](-39\du,10\du)--(-38\du,12\du)--(-36\du,14\du)--(-36\du,16\du)--(-35\du,18\du)--(-32\du,20\du)--(-32\du,22\du)--(-31\du,24\du)--(-30\du,26\du)--(-29\du,28\du)--(-28\du,30\du)--(-25\du,32\du)--(-24\du,34\du)--(-23\du,36\du)--(-23\du,38\du)--(-22\du,40\du)--(-20\du,42\du)--(-18\du,44\du)--(-18\du,46\du)--(-17\du,48\du)--(-15\du,50\du);
+\draw[thick](-15\du,50\du)--(-15\du,51\du)--(-13\du,52\du)--(-12\du,53\du)--(-11\du,54\du)--(-10\du,55\du)--(-9\du,56\du)--(-8\du,57\du)--(-7\du,58\du)--(-7\du,59\du)--(-5\du,60\du);
+\draw[thick](10\du,40\du)--(9\du,42\du)--(6\du,44\du)--(5\du,46\du)--(4\du,48\du)--(3\du,50\du)--(0\du,52\du)--(0\du,54\du)--(-1\du,56\du)--(-4\du,58\du)--(-5\du,60\du);
+\draw[thick](35\du,0\du)--(34\du,2\du)--(33\du,4\du)--(32\du,6\du)--(31\du,8\du)--(30\du,10\du)--(30\du,12\du)--(29\du,14\du)--(27\du,16\du)--(26\du,18\du)--(26\du,20\du)--(24\du,22\du)--(23\du,24\du)--(23\du,26\du)--(22\du,28\du)--(20\du,30\du);
+\draw[thick](20\du,30\du)--(19\du,31\du)--(18\du,32\du)--(17\du,33\du)--(15\du,34\du)--(15\du,35\du)--(14\du,36\du)--(12\du,37\du)--(13\du,38\du)--(10\du,39\du)--(10\du,40\du);
+\draw[thick](-15\du,0\du)--(-15\du,1\du)--(-15\du,3\du)--(-14\du,4\du)--(-14\du,5\du)--(-13\du,7\du)--(-11\du,9\du)--(-11\du,10\du)--(-11\du,11\du)--(-12\du,12\du)--(-11\du,13\du)--(-11\du,14\du)--(-10\du,15\du);
+\draw[thick](-10\du,15\du)--(-8\du,16\du)--(-6\du,17\du)--(-4\du,18\du)--(-2\du,19\du)--(0\du,20\du);
+\draw[thick](0\du,20\du)--(2\du,24\du)--(3\du,26\du)--(4\du,28\du)--(5\du,30\du)--(6\du,32\du)--(8\du,34\du)--(7\du,36\du)--(10\du,38\du)--(10\du,40\du);
+\draw[thick](5\du,0\du)--(5\du,1\du)--(5\du,2\du)--(3\du,5\du)--(3\du,6\du)--(2\du,7\du)--(3\du,8\du)--(2\du,10\du)--(1\du,11\du)--(2\du,12\du)--(1\du,13\du)--(1\du,14\du)--(0\du,15\du);
+\draw[thick](10\du,0\du)--(10\du,1\du)--(8\du,4\du)--(7\du,5\du)--(8\du,6\du)--(8\du,7\du)--(7\du,8\du)--(7\du,10\du)--(6\du,13\du)--(5\du,14\du)--(5\du,15\du);
+\draw[thick](0\du,15\du)--(-2\du,18\du)--(-5\du,19\du)--(-5\du,20\du)--(-7\du,21\du)--(-6\du,22\du)--(-8\du,23\du)--(-9\du,24\du)--(-10\du,25\du)--(-12\du,26\du)--(-12\du,27\du)--(-14\du,28\du)--(-15\du,29\du)--(-15\du,30\du);
+\draw[thick](-15\du,30\du)--(-17\du,35\du)--(-16\du,40\du)--(-14\du,45\du)--(-15\du,50\du);
+\draw[thick](5\du,15\du)--(5\du,17\du)--(5\du,19\du)--(7\du,21\du)--(6\du,23\du)--(6\du,25\du)--(7\du,27\du)--(7\du,29\du)--(8\du,31\du)--(8\du,33\du)--(10\du,35\du)--(10\du,37\du)--(10\du,40\du);
+\draw[thick](-45\du,0\du)--(-44\du,1\du)--(-44\du,2\du)--(-43\du,3\du)--(-42\du,4\du)--(-41\du,5\du)--(-41\du,6\du)--(-40\du,7\du)--(-39\du,8\du)--(-40\du,9\du)--(-39\du,10\du);
+\draw[thick](-50\du,0\du)--(-49\du,1\du)--(-48\du,2\du)--(-45\du,3\du)--(-44\du,4\du)--(-45\du,5\du)--(-44\du,6\du)--(-41\du,7\du)--(-40\du,8\du)--(-39\du,9\du)--(-39\du,10\du);
+\draw[thick,->](-45\du,30\du)--(-36\du,25\du);
+\node at (-45\du,30\du)[above]{\footnotesize species network};
+\draw[thick,->](15\du,55\du)--(6\du,45\du);
+\node at (15\du,55\du)[right]{\footnotesize gene genealogies};
+\draw[thick,->](20\du,50\du)--(11\du,41\du);
+\node at (20\du,50\du)[right]{\footnotesize multiple merger};
+\draw[thick,->](-30\du,55\du)--(-17\du,51\du);
+\draw[thick,->](-30\du,55\du)--(-7\du,60\du);
+\node at (-30\du,55\du)[left]{\footnotesize binary mergers};
+% \node at (-45\du,55\du)[below]{\footnotesize (or Kingman coalescent)};
+% \node at (-30\du,55\du)[left]{\footnotesize multiple merger};
+% \node at (-45\du,55\du)[below]{\footnotesize (or Kingman coalescent)};
+\draw[thick,->](-50\du,15\du)--(-41\du,11\du);
+\node at (-55\du,15\du)[above]{\footnotesize multiple merger};
+\end{tikzpicture}