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| What:| tclfastme: tcl extension based on the FastME phylogeneric tree building program.|

| Where:|  http://www.lbgi.fr/~moumou/|

| Description:| Tcl binding for the FastME program [http://www.ncbi.nlm.nih.gov/CBBresearch/Desper/FastME.html][http://www.ncbi.nlm.nih.gov/pubmed/?term=Fast+and+Accurate+Phylogeny+Reconstruction+Algorithms+Based+on+the+Minimum-Evolution+Principle]. This is a rough tcl-ification of the FastME program, all options are not im<plemented yet.|

| Updated:| 11/2014|
| Contact:| luc.moulinier at unistra.fr|

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** Description : **

Given a list of leaves, and the symmetrical distance matrix linking all the nodes, this extension will compute the corresponding tree using an algorithm based on Minimal Evolution. 

** Usage : **
The minimal form of the tclfastme command is :

fastme ''leavesList'' ''matrixList'' ''?option value? ...''

Given a list of leaves a,b,c, the matrix list is of the form :
======tcl
set matrixList {d(a,a) d(a,b) d(a,c) d(b,a) d(b,b) d(b,c) d(c,a) d(c,b) d(c,c)}
======

where d(a,b) is the distance between a and b, d(a,a) = 0.0.

Three options are currently available :
   * -init_tree (bal)anced|ols|NJ|BIONJ , bal is the default
   * -branch_lengths (bal)anced|OLS , bal is the default
   * -swap (bal)anced|OLS , bal is the default.

Please refer to the reference article for more details on the algorithm [http://www.ncbi.nlm.nih.gov/pubmed/?term=Fast+and+Accurate+Phylogeny+Reconstruction+Algorithms+Based+on+the+Minimum-Evolution+Principle].


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