Some tweaks and ideas to render ancestral sequences aligned to leaf-sequences using ETE3. Resulting image not prefect, but good for data exploration.

ancestral_seq.py

from collections import defaultdict
from ete3 import PhyloTree, TreeStyle, SeqMotifFace, TextFace, RectFace, AttrFace

alg = """
>Dme_001
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEAL--YYASQTDDIKDRREEAH
>Dme_002
MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
>Cfa_001
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
>Mms_001
MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
>Hsa_001
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
>Ptr_002
MAEIPDATIQ-FMALTNVSHNIAVQY--EFGDLNEALNSY--YQTDDQKDRREEAH
>Mmu_002
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
>Hsa_002
MAEAPDETIQQFM-LTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
>Ptr_001
MAEIPDATIQ-FMALTNVSHNIAVQY--EFGDLNEALNSY--YQTDDQKDRREEAH
>Mmu_001
MAEIPDTTIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH

>Ptr_001&Hsa_001&Mmu_001
MAEIPDTTIQXXXALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH

>Ptr_001&Hsa_001
MAEIXXXXXXXXXXXXXXXXXXXXXXXXXXXXLNEALNSYYASQTDDQPDRREEAH

>Cfa_001&Hsa_002&Ptr_001&Ptr_002&Hsa_001&Mmu_001&Mms_001&Mmu_002
MAEIPDTTIQXXXALTNVSHNIAVQYLXXXXXXXXXXXXXXXXxxxxQPDRREEAH


"""

def get_example_tree():
    # Performs a tree reconciliation analysis
    gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),(Ptr_002,(Hsa_002,Mmu_002))));'
    t = PhyloTree(gene_tree_nw)
    ts = TreeStyle()
    # disable default PhyloTree Layout
    ts.layout_fn = lambda x: True
    ts.show_leaf_name = False

    # add phantom branches to all internal nodes. Those phantom branches could
    # show aligned sequences if necessary.
    tmp_node2content = t.get_cached_content(store_attr='name')
    for node in t.get_descendants():
        if not node.is_leaf():
            new_branch = node.add_child()
            new_branch.tag = 'consensus'
            # Phantom names take the name of all their tip names, concatenated
            # in the same order they appear in the tree. Those names will be
            # used to find the ancestral sequence in the fasta file.
            new_branch.name = '&'.join(tmp_node2content[node])
            print new_branch.name
            new_branch.sequence = None
            node.children.reverse()

    t.ladderize() # Improves readability of ancestral seq nodes.

    t.link_to_alignment(alg)
    alg_length = 0
    node2content = t.get_cached_content()
    for node in t.traverse():
        node.img_style["size"] = 0
        if not node.is_leaf():
            pass
        else:
            if getattr(node, "tag", None) == 'consensus':
                # Hide the phantom branch and do not render its name.
                # Alternatively, the branch could be shown with a custom name
                # like 'consensus_seq_XXX'.
                node.img_style['hz_line_color'] = 'white'

                if getattr(node, "sequence", None):
                    f = SeqMotifFace(node.sequence, seq_format="seq", width=6, height=15)
                    f.margin_top = 1
                    f.margin_bottom = 1
                    f.border.color = 'black'
                    f.border.type = 0
                    f.border.width = 2
                    f.background.color = "white"

                    node.add_face(f, column=0, position="aligned")
            else:
                node.add_face(AttrFace('name'), column=0, position='branch-right')
                if getattr(node, "sequence", None):
                    alg_length = max(alg_length, len(node.sequence))
                    f = SeqMotifFace(node.sequence, seq_format="seq", width=6)
                    node.add_face(f, column=0, position="aligned")


    ts.draw_aligned_faces_as_table = False
    for colnum in xrange(alg_length):
        col_f = RectFace(10, 10, fgcolor=None, bgcolor=None,
                         label={"text":str(colnum), "fonttype":"Courier", "color":"black", "fontsize":6})
        ts.aligned_header.add_face(col_f, column=colnum)
    return t, ts

if __name__ == "__main__":
    t, ts = get_example_tree()
    t.show(tree_style=ts)

Note that this is an example dataset. It is not meant to represent anything rather than the illustration layout.