コード例 #1
0
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

    t.link_to_alignment(alg)
    node2content = t.get_cached_content()
    for node in t.traverse():
        node.img_style["size"] = 0

        if not node.is_leaf():
            leaves = node2content[node]
            # get columns with different aa
            subseqs, relevant_columns  = mutation_columns([lf.sequence for lf in leaves])
            for seq in subseqs:
                f = SeqMotifFace(seq, seq_format="seq", width=10, height=8)
                f.margin_top = 2
                f.margin_right = 6
                node.add_face(f, column=0, position="branch-bottom")
            for j, col in enumerate(relevant_columns):
                col_f = RectFace(10, 10, fgcolor=None, bgcolor=None,
                                 label={"text":str(col), "fonttype":"Courier", "color":"black", "fontsize":6})
                node.add_face(col_f, column=j, position="branch-top")
                col_f.margin_bottom = 2
        else:
            f = SeqMotifFace(node.sequence, seq_format="seq", width=6)
            node.add_face(f, column=0, position="aligned")

    alg_length = len(lf.sequence)
    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
コード例 #2
0
ファイル: plot.py プロジェクト: gamcil/fungphy
def get_tree_style(**kwargs):
    style = TreeStyle()
    style.layout_fn = layout
    style.allow_face_overlap = True
    style.branch_vertical_margin = 5
    style.complete_branch_lines_when_necessary = False
    style.draw_aligned_faces_as_table = False
    style.scale = 1500
    style.scale_length = 0.05
    style.show_branch_support = False
    style.show_leaf_name = False

    for key, value in kwargs.items():
        if value == "True":
            value = True
        else:
            try:
                value = float(value)
            except ValueError:
                pass
        setattr(style, key, value)

    return style
コード例 #3
0
ファイル: visualize.py プロジェクト: Ward9250/ete
def draw_tree(tree, conf, outfile):
    try:
        from ete3 import (add_face_to_node, AttrFace, TextFace, TreeStyle, RectFace, CircleFace,
                             SequenceFace, random_color, SeqMotifFace)
    except ImportError as e:
        print(e)
        return

    def ly_basic(node):
        if node.is_leaf():
            node.img_style['size'] = 0
        else:
            node.img_style['size'] = 0
            node.img_style['shape'] = 'square'
            if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"):
                if node.tree_seqtype == "nt":
                    node.img_style["bgcolor"] = "#CFE6CA"
                    ntF = TextFace("nt", fsize=6, fgcolor='#444', ftype='Helvetica')
                    add_face_to_node(ntF, node, 10, position="branch-bottom")
            if len(NPR_TREES) > 1 and hasattr(node, "tree_type"):
                node.img_style['size'] = 4
                node.img_style['fgcolor'] = "steelblue"

        node.img_style['hz_line_width'] = 1
        node.img_style['vt_line_width'] = 1

    def ly_leaf_names(node):
        if node.is_leaf():
            spF = TextFace(node.species, fsize=10, fgcolor='#444444', fstyle='italic', ftype='Helvetica')
            add_face_to_node(spF, node, column=0, position='branch-right')
            if hasattr(node, 'genename'):
                geneF = TextFace(" (%s)" %node.genename, fsize=8, fgcolor='#777777', ftype='Helvetica')
                add_face_to_node(geneF, node, column=1, position='branch-right')

    def ly_supports(node):
        if not node.is_leaf() and node.up:
            supFace = TextFace("%0.2g" %(node.support), fsize=7, fgcolor='indianred')
            add_face_to_node(supFace, node, column=0, position='branch-top')

    def ly_tax_labels(node):
        if node.is_leaf():
            c = LABEL_START_COL
            largest = 0
            for tname in TRACKED_CLADES:
                if hasattr(node, "named_lineage") and tname in node.named_lineage:
                    linF = TextFace(tname, fsize=10, fgcolor='white')
                    linF.margin_left = 3
                    linF.margin_right = 2
                    linF.background.color = lin2color[tname]
                    add_face_to_node(linF, node, c, position='aligned')
                    c += 1

            for n in range(c, len(TRACKED_CLADES)):
                add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'), node, c, position='aligned')
                c+=1

    def ly_full_alg(node):
        pass

    def ly_block_alg(node):
        if node.is_leaf():
            if 'sequence' in node.features:
                seqFace = SeqMotifFace(node.sequence, [])
                # [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
                motifs = []
                last_lt = None
                for c, lt in enumerate(node.sequence):
                    if lt != '-':
                        if last_lt is None:
                            last_lt = c
                        if c+1 == len(node.sequence):
                            start, end = last_lt, c
                            motifs.append([start, end, "()", 0, 12, "slategrey", "slategrey", None])
                            last_lt = None
                    elif lt == '-':
                        if last_lt is not None:
                            start, end = last_lt, c-1
                            motifs.append([start, end, "()", 0, 12, "grey", "slategrey", None])
                            last_lt = None

                seqFace = SeqMotifFace(node.sequence, motifs,
                                       intermotif_format="line",
                                       seqtail_format="line", scale_factor=ALG_SCALE)
                add_face_to_node(seqFace, node, ALG_START_COL, aligned=True)


    TRACKED_CLADES = ["Eukaryota", "Viridiplantae",  "Fungi",
                      "Alveolata", "Metazoa", "Stramenopiles", "Rhodophyta",
                      "Amoebozoa", "Crypthophyta", "Bacteria",
                      "Alphaproteobacteria", "Betaproteobacteria", "Cyanobacteria",
                      "Gammaproteobacteria",]

    # ["Opisthokonta",  "Apicomplexa"]

    colors = random_color(num=len(TRACKED_CLADES), s=0.45)
    lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)])

    NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444')

    LABEL_START_COL = 10
    ALG_START_COL = 40
    ts = TreeStyle()
    ts.draw_aligned_faces_as_table = False
    ts.draw_guiding_lines = False
    ts.show_leaf_name = False
    ts.show_branch_support = False
    ts.scale = 160

    ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels]

    MIXED_RES = set()
    MAX_SEQ_LEN = 0
    NPR_TREES = []
    for n in tree.traverse():
        if hasattr(n, "tree_seqtype"):
            MIXED_RES.add(n.tree_seqtype)
        if hasattr(n, "tree_type"):
            NPR_TREES.append(n.tree_type)
        seq = getattr(n, "sequence", "")
        MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN)

    if MAX_SEQ_LEN:
        ALG_SCALE = min(1, 1000./MAX_SEQ_LEN)
        ts.layout_fn.append(ly_block_alg)

    if len(NPR_TREES) > 1:
        rF = RectFace(4, 4, "steelblue", "steelblue")
        rF.margin_right = 10
        rF.margin_left = 10
        ts.legend.add_face(rF, 0)
        ts.legend.add_face(TextFace(" NPR node"), 1)
        ts.legend_position = 3

    if len(MIXED_RES) > 1:
        rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA")
        rF.margin_right = 10
        rF.margin_left = 10
        ts.legend.add_face(rF, 0)
        ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1)
        ts.legend_position = 3


    try:
        tree.set_species_naming_function(spname)
        annotate_tree_with_ncbi(tree)
        a = tree.search_nodes(species='Dictyostelium discoideum')[0]
        b = tree.search_nodes(species='Chondrus crispus')[0]
        #out = tree.get_common_ancestor([a, b])
        #out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up
        tree.set_outgroup(out)
        tree.swap_children()
    except Exception:
        pass

    tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150)
    tree.render(outfile+'.svg', tree_style=ts, w=170, units='mm', dpi=150)
    tree.render(outfile+'.pdf', tree_style=ts, w=170, units='mm', dpi=150)
コード例 #4
0
ファイル: visualize.py プロジェクト: muppetjones/ete
def draw_tree(tree, conf, outfile):
    try:
        from ete3 import (add_face_to_node, AttrFace, TextFace, TreeStyle,
                          RectFace, CircleFace, SequenceFace, random_color,
                          SeqMotifFace)
    except ImportError as e:
        print(e)
        return

    def ly_basic(node):
        if node.is_leaf():
            node.img_style['size'] = 0
        else:
            node.img_style['size'] = 0
            node.img_style['shape'] = 'square'
            if len(MIXED_RES) > 1 and hasattr(node, "tree_seqtype"):
                if node.tree_seqtype == "nt":
                    node.img_style["bgcolor"] = "#CFE6CA"
                    ntF = TextFace("nt",
                                   fsize=6,
                                   fgcolor='#444',
                                   ftype='Helvetica')
                    add_face_to_node(ntF, node, 10, position="branch-bottom")
            if len(NPR_TREES) > 1 and hasattr(node, "tree_type"):
                node.img_style['size'] = 4
                node.img_style['fgcolor'] = "steelblue"

        node.img_style['hz_line_width'] = 1
        node.img_style['vt_line_width'] = 1

    def ly_leaf_names(node):
        if node.is_leaf():
            spF = TextFace(node.species,
                           fsize=10,
                           fgcolor='#444444',
                           fstyle='italic',
                           ftype='Helvetica')
            add_face_to_node(spF, node, column=0, position='branch-right')
            if hasattr(node, 'genename'):
                geneF = TextFace(" (%s)" % node.genename,
                                 fsize=8,
                                 fgcolor='#777777',
                                 ftype='Helvetica')
                add_face_to_node(geneF,
                                 node,
                                 column=1,
                                 position='branch-right')

    def ly_supports(node):
        if not node.is_leaf() and node.up:
            supFace = TextFace("%0.2g" % (node.support),
                               fsize=7,
                               fgcolor='indianred')
            add_face_to_node(supFace, node, column=0, position='branch-top')

    def ly_tax_labels(node):
        if node.is_leaf():
            c = LABEL_START_COL
            largest = 0
            for tname in TRACKED_CLADES:
                if hasattr(node,
                           "named_lineage") and tname in node.named_lineage:
                    linF = TextFace(tname, fsize=10, fgcolor='white')
                    linF.margin_left = 3
                    linF.margin_right = 2
                    linF.background.color = lin2color[tname]
                    add_face_to_node(linF, node, c, position='aligned')
                    c += 1

            for n in range(c, len(TRACKED_CLADES)):
                add_face_to_node(TextFace('', fsize=10, fgcolor='slategrey'),
                                 node,
                                 c,
                                 position='aligned')
                c += 1

    def ly_full_alg(node):
        pass

    def ly_block_alg(node):
        if node.is_leaf():
            if 'sequence' in node.features:
                seqFace = SeqMotifFace(node.sequence, [])
                # [10, 100, "[]", None, 10, "black", "rgradient:blue", "arial|8|white|domain Name"],
                motifs = []
                last_lt = None
                for c, lt in enumerate(node.sequence):
                    if lt != '-':
                        if last_lt is None:
                            last_lt = c
                        if c + 1 == len(node.sequence):
                            start, end = last_lt, c
                            motifs.append([
                                start, end, "()", 0, 12, "slategrey",
                                "slategrey", None
                            ])
                            last_lt = None
                    elif lt == '-':
                        if last_lt is not None:
                            start, end = last_lt, c - 1
                            motifs.append([
                                start, end, "()", 0, 12, "grey", "slategrey",
                                None
                            ])
                            last_lt = None

                seqFace = SeqMotifFace(node.sequence,
                                       motifs,
                                       intermotif_format="line",
                                       seqtail_format="line",
                                       scale_factor=ALG_SCALE)
                add_face_to_node(seqFace, node, ALG_START_COL, aligned=True)

    TRACKED_CLADES = [
        "Eukaryota",
        "Viridiplantae",
        "Fungi",
        "Alveolata",
        "Metazoa",
        "Stramenopiles",
        "Rhodophyta",
        "Amoebozoa",
        "Crypthophyta",
        "Bacteria",
        "Alphaproteobacteria",
        "Betaproteobacteria",
        "Cyanobacteria",
        "Gammaproteobacteria",
    ]

    # ["Opisthokonta",  "Apicomplexa"]

    colors = random_color(num=len(TRACKED_CLADES), s=0.45)
    lin2color = dict([(ln, colors[i]) for i, ln in enumerate(TRACKED_CLADES)])

    NAME_FACE = AttrFace('name', fsize=10, fgcolor='#444444')

    LABEL_START_COL = 10
    ALG_START_COL = 40
    ts = TreeStyle()
    ts.draw_aligned_faces_as_table = False
    ts.draw_guiding_lines = False
    ts.show_leaf_name = False
    ts.show_branch_support = False
    ts.scale = 160

    ts.layout_fn = [ly_basic, ly_leaf_names, ly_supports, ly_tax_labels]

    MIXED_RES = set()
    MAX_SEQ_LEN = 0
    NPR_TREES = []
    for n in tree.traverse():
        if hasattr(n, "tree_seqtype"):
            MIXED_RES.add(n.tree_seqtype)
        if hasattr(n, "tree_type"):
            NPR_TREES.append(n.tree_type)
        seq = getattr(n, "sequence", "")
        MAX_SEQ_LEN = max(len(seq), MAX_SEQ_LEN)

    if MAX_SEQ_LEN:
        ALG_SCALE = min(1, 1000. / MAX_SEQ_LEN)
        ts.layout_fn.append(ly_block_alg)

    if len(NPR_TREES) > 1:
        rF = RectFace(4, 4, "steelblue", "steelblue")
        rF.margin_right = 10
        rF.margin_left = 10
        ts.legend.add_face(rF, 0)
        ts.legend.add_face(TextFace(" NPR node"), 1)
        ts.legend_position = 3

    if len(MIXED_RES) > 1:
        rF = RectFace(20, 20, "#CFE6CA", "#CFE6CA")
        rF.margin_right = 10
        rF.margin_left = 10
        ts.legend.add_face(rF, 0)
        ts.legend.add_face(TextFace(" Nucleotide based alignment"), 1)
        ts.legend_position = 3

    try:
        tree.set_species_naming_function(spname)
        annotate_tree_with_ncbi(tree)
        a = tree.search_nodes(species='Dictyostelium discoideum')[0]
        b = tree.search_nodes(species='Chondrus crispus')[0]
        #out = tree.get_common_ancestor([a, b])
        #out = tree.search_nodes(species='Haemophilus parahaemolyticus')[0].up
        tree.set_outgroup(out)
        tree.swap_children()
    except Exception:
        pass

    tree.render(outfile, tree_style=ts, w=170, units='mm', dpi=150)
    tree.render(outfile + '.svg', tree_style=ts, w=170, units='mm', dpi=150)
    tree.render(outfile + '.pdf', tree_style=ts, w=170, units='mm', dpi=150)
コード例 #5
0
ファイル: mktreefig.py プロジェクト: argriffing/phyly
>0
AAATGGCTGTGCACGTC
>1
GACTGGATCTGCACGTC
>2
CTCTGGATGTGCACGTG
>3
AAATGGCGGTGCGCCTA
"""

t = PhyloTree(nw, alignment=fa, alg_format='fasta', format=1)
ts = TreeStyle()
ts.show_branch_length = False
ts.show_leaf_name = False
ts.draw_guiding_lines = True
ts.draw_aligned_faces_as_table = True
ts.show_scale = False


def my_layout(node):
    #
    # add names to all nodes (not just to leaf nodes)
    # ete3/test/test_treeview/face_rotation.py
    F = TextFace(node.name, tight_text=True)
    add_face_to_node(F, node, column=0, position="branch-right")
    #
    # add branch lengths
    # ete3/treeview/qt4_render.py
    if not node.is_root():
        bl_face = AttrFace("dist",
                           fsize=8,
コード例 #6
0
ファイル: mktreefig.py プロジェクト: argriffing/phyly
from ete3 import add_face_to_node, TextFace, AttrFace, SequenceFace

nw = '(0:0, 1:20);'
fa = """
>0
AA..
>1
CAA.
"""

t = PhyloTree(nw, alignment=fa, alg_format='fasta', format=1)
ts = TreeStyle()
ts.show_branch_length = False
ts.show_leaf_name = False
ts.draw_guiding_lines = True
ts.draw_aligned_faces_as_table = True
ts.show_scale = False

def my_layout(node):
    #
    # add names to all nodes (not just to leaf nodes)
    # ete3/test/test_treeview/face_rotation.py
    F = TextFace(node.name, tight_text=True)
    add_face_to_node(F, node, column=0, position="branch-right")
    #
    # add branch lengths
    # ete3/treeview/qt4_render.py
    if not node.is_root():
        bl_face = AttrFace("dist", fsize=8, ftype="Arial",
                fgcolor="black", formatter="%0.3g")
        #
コード例 #7
0
    def render(self,
               outfile,
               idlabel=False,
               isolabel=False,
               colormap=None,
               chain_split=None):
        '''Render to image file, filetype inferred from suffix, svg for color images'''
        def my_layout(node):
            circle_color = 'lightgray' if colormap is None or node.name not in colormap else colormap[
                node.name]
            text_color = 'black'
            if isinstance(circle_color, str):
                if isolabel and hasattr(node, 'isotype'):
                    nl = ''.join(
                        sorted(set([ISO_SHORT[iss] for iss in node.isotype]),
                               key=lambda x: ISO_TYPE_charORDER[x]))
                else:
                    nl = str(node.frequency)
                C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
                               color=circle_color,
                               label={
                                   'text': nl,
                                   'color': text_color
                               } if node.frequency > 0 else None)
                C.rotation = -90
                C.hz_align = 1
                faces.add_face_to_node(C, node, 0)
            else:
                P = PieChartFace(
                    [100 * x / node.frequency for x in circle_color.values()],
                    2 * 10 * scipy.sqrt(node.frequency),
                    2 * 10 * scipy.sqrt(node.frequency),
                    colors=[(color if color != 'None' else 'lightgray')
                            for color in list(circle_color.keys())],
                    line_color=None)
                T = TextFace(' '.join(
                    [str(x) for x in list(circle_color.values())]),
                             tight_text=True)
                T.hz_align = 1
                T.rotation = -90
                faces.add_face_to_node(P, node, 0, position='branch-right')
                faces.add_face_to_node(T, node, 1, position='branch-right')
            if idlabel:
                T = TextFace(node.name, tight_text=True, fsize=6)
                T.rotation = -90
                T.hz_align = 1
                faces.add_face_to_node(
                    T,
                    node,
                    1 if isinstance(circle_color, str) else 2,
                    position='branch-right')
            elif isolabel and hasattr(node, 'isotype') and False:
                iso_name = ''.join(
                    sorted(set([ISO_SHORT[iss] for iss in node.isotype]),
                           key=lambda x: ISO_TYPE_charORDER[x]))
                #T = TextFace(iso_name, tight_text=True, fsize=6)
                #T.rotation = -90
                #T.hz_align = 1
                #faces.add_face_to_node(T, node, 1 if isinstance(circle_color, str) else 2, position='branch-right')
                C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
                               color=circle_color,
                               label={
                                   'text': iso_name,
                                   'color': text_color
                               } if node.frequency > 0 else None)
                C.rotation = -90
                C.hz_align = 1
                faces.add_face_to_node(C, node, 0)

        for node in self.tree.traverse():
            nstyle = NodeStyle()
            nstyle['size'] = 0
            if node.up is not None:
                if set(node.sequence.upper()) == set(
                        'ACGT'):  # Don't know what this do, try and delete
                    aa = translate(node.sequence)
                    aa_parent = translate(node.up.sequence)
                    nonsyn = hamming_distance(aa, aa_parent)
                    if '*' in aa:
                        nstyle['bgcolor'] = 'red'
                    if nonsyn > 0:
                        nstyle['hz_line_color'] = 'black'
                        nstyle['hz_line_width'] = nonsyn
                    else:
                        nstyle['hz_line_type'] = 1
            node.set_style(nstyle)

        ts = TreeStyle()
        ts.show_leaf_name = False
        ts.rotation = 90
        ts.draw_aligned_faces_as_table = False
        ts.allow_face_overlap = True
        ts.layout_fn = my_layout
        ts.show_scale = False
        self.tree.render(outfile, tree_style=ts)
        # If we labelled seqs, let's also write the alignment out so we have the sequences (including of internal nodes):
        if idlabel:
            aln = MultipleSeqAlignment([])
            for node in self.tree.traverse():
                aln.append(
                    SeqRecord(Seq(str(node.sequence), generic_dna),
                              id=node.name,
                              description='abundance={}'.format(
                                  node.frequency)))
            AlignIO.write(aln,
                          open(os.path.splitext(outfile)[0] + '.fasta', 'w'),
                          'fasta')
コード例 #8
0
    def render(self,
               outfile,
               idlabel=False,
               colormap=None,
               show_support=False,
               chain_split=None):
        '''render to image file, filetype inferred from suffix, svg for color images'''
        def my_layout(node):
            circle_color = 'lightgray' if colormap is None or node.name not in colormap else colormap[
                node.name]
            text_color = 'black'
            if isinstance(circle_color, str):
                C = CircleFace(radius=max(3, 10 * scipy.sqrt(node.frequency)),
                               color=circle_color,
                               label={
                                   'text': str(node.frequency),
                                   'color': text_color
                               } if node.frequency > 0 else None)
                C.rotation = -90
                C.hz_align = 1
                faces.add_face_to_node(C, node, 0)
            else:
                P = PieChartFace(
                    [100 * x / node.frequency for x in circle_color.values()],
                    2 * 10 * scipy.sqrt(node.frequency),
                    2 * 10 * scipy.sqrt(node.frequency),
                    colors=[(color if color != 'None' else 'lightgray')
                            for color in list(circle_color.keys())],
                    line_color=None)
                T = TextFace(' '.join(
                    [str(x) for x in list(circle_color.values())]),
                             tight_text=True)
                T.hz_align = 1
                T.rotation = -90
                faces.add_face_to_node(P, node, 0, position='branch-right')
                faces.add_face_to_node(T, node, 1, position='branch-right')
            if idlabel:
                T = TextFace(node.name, tight_text=True, fsize=6)
                T.rotation = -90
                T.hz_align = 1
                faces.add_face_to_node(
                    T,
                    node,
                    1 if isinstance(circle_color, str) else 2,
                    position='branch-right')

        for node in self.tree.traverse():
            nstyle = NodeStyle()
            nstyle['size'] = 0
            if node.up is not None:
                if set(node.sequence.upper()) == set('ACGT'):
                    if chain_split is not None:
                        if self.frame is not None:
                            raise NotImplementedError(
                                'frame not implemented with chain_split')
                        leftseq_mutated = hamming_distance(
                            node.sequence[:chain_split],
                            node.up.sequence[:chain_split]) > 0
                        rightseq_mutated = hamming_distance(
                            node.sequence[chain_split:],
                            node.up.sequence[chain_split:]) > 0
                        if leftseq_mutated and rightseq_mutated:
                            nstyle['hz_line_color'] = 'purple'
                            nstyle['hz_line_width'] = 3
                        elif leftseq_mutated:
                            nstyle['hz_line_color'] = 'red'
                            nstyle['hz_line_width'] = 2
                        elif rightseq_mutated:
                            nstyle['hz_line_color'] = 'blue'
                            nstyle['hz_line_width'] = 2
                    if self.frame is not None:
                        aa = Seq(
                            node.sequence[(self.frame -
                                           1):(self.frame - 1 +
                                               (3 *
                                                (((len(node.sequence) -
                                                   (self.frame - 1)) // 3))))],
                            generic_dna).translate()
                        aa_parent = Seq(
                            node.up.sequence[(self.frame -
                                              1):(self.frame - 1 + (3 * ((
                                                  (len(node.sequence) -
                                                   (self.frame - 1)) // 3))))],
                            generic_dna).translate()
                        nonsyn = hamming_distance(aa, aa_parent)
                        if '*' in aa:
                            nstyle['bgcolor'] = 'red'
                        if nonsyn > 0:
                            nstyle['hz_line_color'] = 'black'
                            nstyle['hz_line_width'] = nonsyn
                        else:
                            nstyle['hz_line_type'] = 1
            node.set_style(nstyle)

        ts = TreeStyle()
        ts.show_leaf_name = False
        ts.rotation = 90
        ts.draw_aligned_faces_as_table = False
        ts.allow_face_overlap = True
        ts.layout_fn = my_layout
        ts.show_scale = False
        ts.show_branch_support = show_support
        self.tree.render(outfile, tree_style=ts)
        # if we labelled seqs, let's also write the alignment out so we have the sequences (including of internal nodes)
        if idlabel:
            aln = MultipleSeqAlignment([])
            for node in self.tree.traverse():
                aln.append(
                    SeqRecord(Seq(str(node.sequence), generic_dna),
                              id=str(node.name),
                              description='abundance={}'.format(
                                  node.frequency)))
            AlignIO.write(aln,
                          open(os.path.splitext(outfile)[0] + '.fasta', 'w'),
                          'fasta')