The FMTS program can be used to compare two trees, one or both of which are multigene family trees. The FMTS program obtains all the single-gene trees from one multi-gene famly tree or randomly prunes the multi-gene family tree to obtain some single gene family trees. By default, this is done 100 times (the user can modify the number of repetitions). Then each single-gene family tree is used to make the comparison and the result of the FMTS program is the mean and standard deviation of all of the comparisons.

         How to run: the program automatically detects whether a tree belongs to a multigene family. The parameter '-s' modifies the number of single-gene trees.

         The use of the FMTS program may be computationally expensive when the number of single-gene family trees obtained from a multi-gene family tree is enormous. Click here to see how the number of single-gene family trees increases with the number of genes with more than one copy and the number of copies.

         From one multi-family tree we can obtain many single trees. The following example shows how from one multi-family tree with 5 taxa (3 of the taxa with more than one copy), 12 single trees can be constructed. Click here to see the example.