This a basic manual for the Lasso approach as described in 

``Reconstructing (Super)trees from data sets with missing distances: 
Not all is lost''

by G. Kettleborough, J. Dicks, I. N. Roberts and K. T. Huber.

The program comes with an example file 
and currently runs on Windows 7. Given a (partial or complete)
distance D on some set X of taxa, it aims to finds a subset L'  of 
cords of the set of cords of X induced by D  and
an equidistant Y-tree (T,w) that is strongly lassoed by it such that
Y and L' are as large as possible, Y is is the union of the elements in
the cords of L' and, for all cords xy \in L'
we have that D(x,y) equals the distance between x and y induced by (T,w)
Lasso can display the found
tree on either on the computer screen, save it in a .tex file
or in Newick format which can be read by other phylogenetic tree
reconstruction tools such as PHYLIP.

Folder containing the Lasso software is called 
lasso-win32.zip and contains the files: 

lasso.exe paradoxus-part.csv  README.txt   run-lasso.bat

where paradoxus-part.csv is an example file.

The input to Lasso is a (partial or complete) distance 
matrix in the form of a .CSV file with a header where he value ? represents
a missing value (see the included paradoxus-part.csv file for an example).

Currently, the Lasso software can be run in two different ways
one of which is comand line based and the other is to double click
on run-lasso.bat. 

COMMANDLINE:

Assuming that the user is in the folder that contains "lasso.exe"
the first step is to execute lasso which is done by typing in

lasso input matrix -t > output

where input matrix is the partial distance matrix and output is
the file that contains the genrated tree. For the above example file
this is
 
lasso paradoxus-part.csv -t > output

The parameter -t determines what happens to the output file.
If "-t" is kept then the output is written in the specified
output file (which must have extension .tex) which can then be fed
into the drawing routine below which is based on latex. To do this
you need to have latex installed on your computer. If this is the
case then copy the text below starting with 
"\documentclass[a4paper,10pt]{article}" and ending with 
"\end{document}" into a separte file called result.tex. In
result.tex replace  "\input{tree.tex}" by  "\input{yourtree.tex}"
where "yourtree.tex" contains the output generated by Lasso. 

Te result.tex file contains two options to display the generated tree.
the first one dispalys the tree in the stuandard way (see e.g.e Fig 5 
in paper) whereas thr second displays the generated tree in circular 
form (see e.g. Fig 6) in the above paper. 

-----------------------------

\documentclass[a4paper,10pt]{article}

\usepackage{tikz}

\usetikzlibrary{calc}

\begin{document}

\begin{tikzpicture}[xscale=50,yscale=0.5]
  \input{tree.tex}
\end{tikzpicture}


\begin{tikzpicture}[scale=5]
  \input{tree-polar.tex}
\end{tikzpicture}

\end{document}

Note the scale parameters for tikzpicture.  You will need to play around with
these to make the picture look nice in your document.  If you need to change
the size of the labels, use scalefont, e.g.:

{\scalefont{0.3}
\begin{tikzpicture}[scale=22]
  \input{tree-polar.tex}
\end{tikzpicture}
}

------------------------------

Note the scale parameters for tikzpicture.  You will need to play around with
these to make the picture look nice in your document.  If you need to change
the size of the labels, use scalefont, e.g.:

{\scalefont{0.3}
\begin{tikzpicture}[scale=22]
  \input{tree-polar.tex}
\end{tikzpicture}
}


RUN-LASSO.BAT:

Using this option, "run-lasso.bat" has to be double clicked
which generates a window in which first the input matrix needs to be
entered and then the file that will contain the output. In this
option ......