A phylogenetic tree (evolutionary tree) visualization showing hierarchical relationships between species or sequences, with branch lengths proportional to evolutionary distance. This diagram reveals how organisms or genes evolved from common ancestors, with longer branches indicating greater divergence. Phylogenetic trees are essential for understanding evolutionary history, taxonomy, and molecular biology relationships.
""" anyplot.ai
tree-phylogenetic: Phylogenetic Tree Diagram
Library: plotnine 0.15.4 | Python 3.13.13
Quality: 90/100 | Updated: 2026-05-15
"""
import os
import numpy as np
import pandas as pd
from plotnine import (
aes,
annotate,
coord_cartesian,
element_blank,
element_rect,
element_text,
geom_point,
geom_segment,
geom_text,
ggplot,
labs,
scale_color_manual,
theme,
theme_void,
)
THEME = os.getenv("ANYPLOT_THEME", "light")
PAGE_BG = "#FAF8F1" if THEME == "light" else "#1A1A17"
INK = "#1A1A17" if THEME == "light" else "#F0EFE8"
INK_SOFT = "#4A4A44" if THEME == "light" else "#B8B7B0"
IMPRINT = ["#009E73", "#C475FD", "#4467A3", "#BD8233", "#AE3030", "#2ABCCD", "#954477"]
np.random.seed(42)
# Phylogenetic tree data for primate evolution (mitochondrial DNA based)
species = ["Human", "Chimpanzee", "Gorilla", "Orangutan", "Gibbon", "Macaque", "Baboon", "Lemur"]
n_species = len(species)
leaf_y = {species[i]: i for i in range(n_species)}
branch_data = {
"root": 0.0,
"haplorrhini": 0.15,
"strepsirrhini": 0.15,
"catarrhini": 0.25,
"hylobatidae": 0.25,
"hominoidea": 0.35,
"cercopithecidae": 0.35,
"homininae": 0.45,
"ponginae": 0.45,
"hominini": 0.55,
"gorillini": 0.55,
}
leaf_x = {
"Human": 0.65,
"Chimpanzee": 0.65,
"Gorilla": 0.60,
"Orangutan": 0.55,
"Gibbon": 0.50,
"Macaque": 0.55,
"Baboon": 0.55,
"Lemur": 0.45,
}
internal_y = {
"hominini": (leaf_y["Human"] + leaf_y["Chimpanzee"]) / 2,
"gorillini": leaf_y["Gorilla"],
"homininae": (leaf_y["Human"] + leaf_y["Chimpanzee"] + leaf_y["Gorilla"]) / 3,
"ponginae": leaf_y["Orangutan"],
"hominoidea": (leaf_y["Human"] + leaf_y["Chimpanzee"] + leaf_y["Gorilla"] + leaf_y["Orangutan"]) / 4,
"hylobatidae": leaf_y["Gibbon"],
"catarrhini": (leaf_y["Human"] + leaf_y["Chimpanzee"] + leaf_y["Gorilla"] + leaf_y["Orangutan"] + leaf_y["Gibbon"])
/ 5,
"cercopithecidae": (leaf_y["Macaque"] + leaf_y["Baboon"]) / 2,
"haplorrhini": (
leaf_y["Human"]
+ leaf_y["Chimpanzee"]
+ leaf_y["Gorilla"]
+ leaf_y["Orangutan"]
+ leaf_y["Gibbon"]
+ leaf_y["Macaque"]
+ leaf_y["Baboon"]
)
/ 7,
"strepsirrhini": leaf_y["Lemur"],
"root": sum(leaf_y.values()) / len(leaf_y),
}
segments = [
{
"x": branch_data["root"],
"xend": branch_data["haplorrhini"],
"y": internal_y["haplorrhini"],
"yend": internal_y["haplorrhini"],
"clade": "Haplorrhini",
},
{
"x": branch_data["root"],
"xend": branch_data["strepsirrhini"],
"y": internal_y["strepsirrhini"],
"yend": internal_y["strepsirrhini"],
"clade": "Strepsirrhini",
},
{
"x": branch_data["root"],
"xend": branch_data["root"],
"y": internal_y["haplorrhini"],
"yend": internal_y["strepsirrhini"],
"clade": "Root",
},
{
"x": branch_data["strepsirrhini"],
"xend": leaf_x["Lemur"],
"y": leaf_y["Lemur"],
"yend": leaf_y["Lemur"],
"clade": "Strepsirrhini",
},
{
"x": branch_data["haplorrhini"],
"xend": branch_data["catarrhini"],
"y": internal_y["catarrhini"],
"yend": internal_y["catarrhini"],
"clade": "Haplorrhini",
},
{
"x": branch_data["haplorrhini"],
"xend": branch_data["catarrhini"],
"y": internal_y["cercopithecidae"],
"yend": internal_y["cercopithecidae"],
"clade": "Haplorrhini",
},
{
"x": branch_data["haplorrhini"],
"xend": branch_data["haplorrhini"],
"y": internal_y["catarrhini"],
"yend": internal_y["cercopithecidae"],
"clade": "Haplorrhini",
},
{
"x": branch_data["catarrhini"],
"xend": branch_data["hominoidea"],
"y": internal_y["hominoidea"],
"yend": internal_y["hominoidea"],
"clade": "Hominoidea",
},
{
"x": branch_data["catarrhini"],
"xend": leaf_x["Gibbon"],
"y": leaf_y["Gibbon"],
"yend": leaf_y["Gibbon"],
"clade": "Hylobatidae",
},
{
"x": branch_data["catarrhini"],
"xend": branch_data["catarrhini"],
"y": internal_y["hominoidea"],
"yend": leaf_y["Gibbon"],
"clade": "Catarrhini",
},
{
"x": branch_data["catarrhini"],
"xend": leaf_x["Macaque"],
"y": leaf_y["Macaque"],
"yend": leaf_y["Macaque"],
"clade": "Cercopithecidae",
},
{
"x": branch_data["catarrhini"],
"xend": leaf_x["Baboon"],
"y": leaf_y["Baboon"],
"yend": leaf_y["Baboon"],
"clade": "Cercopithecidae",
},
{
"x": branch_data["catarrhini"],
"xend": branch_data["catarrhini"],
"y": leaf_y["Macaque"],
"yend": leaf_y["Baboon"],
"clade": "Cercopithecidae",
},
{
"x": branch_data["hominoidea"],
"xend": branch_data["homininae"],
"y": internal_y["homininae"],
"yend": internal_y["homininae"],
"clade": "Homininae",
},
{
"x": branch_data["hominoidea"],
"xend": leaf_x["Orangutan"],
"y": leaf_y["Orangutan"],
"yend": leaf_y["Orangutan"],
"clade": "Ponginae",
},
{
"x": branch_data["hominoidea"],
"xend": branch_data["hominoidea"],
"y": internal_y["homininae"],
"yend": leaf_y["Orangutan"],
"clade": "Hominoidea",
},
{
"x": branch_data["homininae"],
"xend": branch_data["hominini"],
"y": internal_y["hominini"],
"yend": internal_y["hominini"],
"clade": "Hominini",
},
{
"x": branch_data["homininae"],
"xend": leaf_x["Gorilla"],
"y": leaf_y["Gorilla"],
"yend": leaf_y["Gorilla"],
"clade": "Gorillini",
},
{
"x": branch_data["homininae"],
"xend": branch_data["homininae"],
"y": internal_y["hominini"],
"yend": leaf_y["Gorilla"],
"clade": "Homininae",
},
{
"x": branch_data["hominini"],
"xend": leaf_x["Human"],
"y": leaf_y["Human"],
"yend": leaf_y["Human"],
"clade": "Hominini",
},
{
"x": branch_data["hominini"],
"xend": leaf_x["Chimpanzee"],
"y": leaf_y["Chimpanzee"],
"yend": leaf_y["Chimpanzee"],
"clade": "Hominini",
},
{
"x": branch_data["hominini"],
"xend": branch_data["hominini"],
"y": leaf_y["Human"],
"yend": leaf_y["Chimpanzee"],
"clade": "Hominini",
},
]
df_segments = pd.DataFrame(segments)
df_leaves = pd.DataFrame({"x": [leaf_x[s] for s in species], "y": [leaf_y[s] for s in species], "species": species})
clade_colors = {
"Root": "#999999",
"Strepsirrhini": IMPRINT[0],
"Haplorrhini": IMPRINT[1],
"Catarrhini": IMPRINT[2],
"Hylobatidae": IMPRINT[3],
"Hominoidea": IMPRINT[4],
"Cercopithecidae": IMPRINT[5],
"Homininae": IMPRINT[6],
"Ponginae": IMPRINT[0],
"Gorillini": IMPRINT[1],
"Hominini": IMPRINT[2],
}
df_segments["color"] = df_segments["clade"].map(clade_colors)
plot = (
ggplot()
+ geom_segment(df_segments, aes(x="x", xend="xend", y="y", yend="yend", color="clade"), size=2.5)
+ geom_point(df_leaves, aes(x="x", y="y"), size=5, color=IMPRINT[0])
+ geom_text(df_leaves, aes(x="x", y="y", label="species"), ha="left", nudge_x=0.02, size=14, color=INK)
+ scale_color_manual(values=clade_colors)
+ annotate("segment", x=0.0, xend=0.1, y=-0.8, yend=-0.8, size=2.5, color=INK_SOFT)
+ annotate("text", x=0.05, y=-1.3, label="0.1 substitutions/site", size=16, color=INK_SOFT)
+ labs(title="tree-phylogenetic · plotnine · anyplot.ai", x="Evolutionary Distance (substitutions per site)")
+ coord_cartesian(xlim=(-0.05, 0.85), ylim=(-1.5, 7.5))
+ theme_void()
+ theme(
figure_size=(16, 9),
plot_background=element_rect(fill=PAGE_BG, color=PAGE_BG),
plot_title=element_text(size=24, ha="center", color=INK),
legend_position=(0.88, 0.75),
legend_background=element_rect(fill=PAGE_BG, alpha=0.95),
legend_title=element_text(size=14, color=INK),
legend_text=element_text(size=12, color=INK_SOFT),
legend_key=element_blank(),
plot_margin=0.05,
)
+ labs(color="Clade")
)
plot.save(f"plot-{THEME}.png", dpi=300, verbose=False)
Part of Phylogenetic Tree Diagram on anyplot.ai.