T.get_evol_model('M2').set_histface(kind='curve', colors=col, up = False, hlines=[1.0,0.3], hlines_col=['black','grey']) T.show(histfaces = ['M1', 'M2']) ### # mark tree functionality print T.write(format=10) name = None while name not in T.get_leaf_names(): name = raw_input(' ====> As you need to mark some branches to run branch\n\ models, type the name of one leaf: ') idname = T.get_leaves_by_name(name)[0].node_id print ' ----> you want to mark:',name,'that has this idname: ', idname T.mark_tree([idname]) # by default will mark with '#1' print 'have a look to the mark: ' print re.sub('#','|',re.sub('[0-9a-zA-Z_(),;]',' ',T.write(format=10))) print re.sub('#','v',re.sub('[0-9a-zA-Z_(),;]',' ',T.write(format=10))) print T.write(format=10) print '\n You have marked the tree with a command like: T.mark_tree([%d])\n' % (idname) print '\n%s\n%s\n%s\n' % ('*'*10 + ' doc ' + '*'*10, T.mark_tree.func_doc, \ '*'*30) print '\n\n\n ----> We are now going to run branch-site models bsA and bsA1:\n\n' raw_input(" ====> hit some key to start computation with our marked tree") for model in ['bsA','bsA1']: print 'running model ' + model
T.get_evol_model ('M2').set_histface (typ='protamine', col=col, up = False, lines=[1.0,0.3], col_lines=['black','grey']) T.show (histfaces = ['M1', 'M2']) ### # mark tree functionality print T.write(format=10) name = None while name not in T.get_leaf_names(): name = raw_input(' ====> As you need to mark some branches to run branch\n\ models, type the name of one leaf: ') idname = T.get_leaves_by_name(name)[0]._nid print ' ----> you want to mark:',name,'that has this idname: ', idname T.mark_tree([idname]) # by default will mark with '#1' print 'have a look to the mark: ' print re.sub('#','|',re.sub('[0-9a-zA-Z_(),;]',' ',T.write(format=10))) print re.sub('#','v',re.sub('[0-9a-zA-Z_(),;]',' ',T.write(format=10))) print T.write(format=10) print '\n You have marked the tree with a command like: T.mark_tree([%d])\n' % (idname) print '\n%s\n%s\n%s\n' % ('*'*10 + ' doc ' + '*'*10, T.mark_tree.func_doc, \ '*'*30) print '\n\n\n ----> We are now going to run branch-site models bsA and bsA1:\n\n' raw_input(" ====> hit some key to start computation with our marked tree") for model in ['bsA','bsA1']: print 'running model ' + model