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
