1.3 addquart - phylogeny reconstruction from a set of quartets and a partially resolved tree Berry phylogeny addquart addquart perl "addquart" 0 bipfile bipfile: contains the edges of the tree T to complete perl "ln -s $bipfile bipfile; " -10 Contains the number of taxa, the association of a number to each taxa, then the edges of the tree T to complete, coded as the bipartitions (splits) they induce on the taxa, eg: 1 2 3 | 4 5 6 corresponds to the edge separating taxa 1, 2 and 3 from taxa 4,5 and 6. This file can be computed by qstar program of the same package. bipfile perl 1 bipfile quartfile_left quartfile_res quartfile_left quartfile.left: contains the set of quartets unresolved by the tree T perl "ln -s $quartfile_left quartfile.left; " -10 Contains the set Q' of quartets unresolved by the tree T and which are to be respected as much as possible when extending the tree T. This file is computed by the qstar program of the same package in a previous step. quartfile_res quartfile.res: contains the set of satisfied quartets perl ($value)? "ln -s $quartfile_res quartfile.res; " : "" -10 If present, this file is used to add the number of quartets of Q* to the number of quartets satisfied by the tree inferred by AddQuart. Otherwise, AddQuart only indicates the number of quartets of Q' satisfied by the output tree. This file is computed by the qstar program of the same package in a previous step. outbipfile bipfile tree_pop perl " ;tree-pop" 2 treefile treefile phylip_tree perl 1