Updated 2014-11-18 18:26:45 by ak

What: tclfastme: tcl extension based on the FastME phylogenetic tree building program.
Where: http://www.lbgi.fr/~moumou/
Description: Tcl binding for the FastME program [1][2]. This is a rough tcl-ification of the FastME program, all options are not implemented yet.
Updated: 11/2014
Contact: luc.moulinier at unistra.fr

Description :  edit

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 :  edit

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 :
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 [3].