LSD: LEAST-SQUARES METHODS TO ESTIMATE RATES AND DATES FROM SERIAL PHYLOGENIES - v0.2 by Thu-Hien TO

If you use this software, please cite: “ Fast dating using least-squares criteria and algorithms”, T-H. To, M. Jung, S. Lycett, O. Gascuel. 

The program can be downloaded at http://www.atgc-montpellier.fr/LSD/

The windows executable file which can be opened by double-click is at bin/lsd_win.exe

How To Compile LSD:
     Use g++ compiler to compile the program from the code source (just standard C++ libaries are needed). From the terminal:
	 >./configure
	 >make
     Then, if you wish to install the program on your system, type:
	 >make install
     or  >sudo make install
How to Run LSD:
	After compiled the program, from the directory that contains the executable file (normally the src directory):
		if you want to use use the interface, type ./lsd
		if you want to use the command line, type ./lsd -i <"input_tree_file"> -d <"input_date_file"> (to estimate absolute dates)
		                                       or ./lsd -i <"input_tree_file"> -a root_date -z leaves_date (to estimate relative dates)
			further options can be specified (-o -c -v -n -r -g ...). Type "./lsd -h" for help. Option -c is recommended to take into account the temporal constraints (date of a node >= date of its ancestors).
	If the program is installed or the path of the executable file is added into PATH, you can run it from anywhere by typing lsd (and with or without options).		

Some examples:

1) Examples of command line:
for rooted tree, constrained mode, and using variances
./lsd -i rootedtree_file -d date_file -c -v
for rooted tree, constrained mode, re-estimate the root position around the given root, and non variances
./lsd -i rootedtree_file -d date_file -c -r l
for unrooted tree without outgroups, without constraints, estimate the root position, and using variances
./lsd -i unrootedtree_file -d date_file -c -v -r a
for unrooted tree with outgroups, constrained mode, using varainces, remove outgroups to obtain the root
./lsd -i unrootedtree_file -d date_file -g outgroup_file -c -v
for rooted tree, constrained mode, using variances, and using given rates to estimate dates
./lsd -i rootedtree_file -d date_file -w given_rate_file -c -v
for rooted tree, estimating relative dates with date root=0 and date of all leaves=1, using variances, with constraint
./lsd -i tree_file -c -v -a 0 -z 1

2) Examples of input files:
Example of Input_tree_file format (newick)
	(a:0.12,(b:0.3,c:0.5):0.4);
	((a:0.12,b:0.3):0.7,c:0.5);	
Example of Input_date_file format:
	3
	a 1999
	b 2000
	c 1780
Example of Outgroup_file format:
	2
	outgroup1
	outgroup2
Example of given_rate_file format:
	0.0068
	0.0052
3) Output files: 
.result : contain the estimated rate, root date and the value of the log likelihood function if variances are used.
.newick : trees in newick format with the new branch length (re-estimated by the program).
.date.newick : trees in newick format where branch lengths are measured rescaled to time unit by multiplying with the estimated rate. 
.nexus : trees in nexus format which contain both information about the dates of internal nodes and branch lengths.