Frequency chaos game method and fractals show evolutionary relationships of the PRKN gene in primates

Supplementary Material: 01 Supplementary Material: Contains an Excel file named “Frequency and relative frequency of nucleotides in primate PRKN” with the nucleotide relative and total frequency for each species. Moreover, the individual nucleotide relative and total frequency are represented in bar charts graphics and are located in two separated subfolders named “01 PRKN nucleotide relative frequency” and “02 PRKN nucleotide total frequency” respectively, with the name of each species. 02 Supplementary Material: Contains the graphic representation of the fractals generated for the 16 PRKN sequences of primates. The graphics are located in 16 subfolders labeled with each primate scientific name. Each one contains 9 images that corresponded to k-mers from 3 to 11, and were generated by the "Frequency Chaos Game Representation" methodology. These were titled with the name of the species, the letter “k” and the corresponding number of "K-mers". Likewise, the order of the quadrants to form the fractal was: Upper, Guanine – Thymine and Lower, Cytosine – Adenine. 03 Supplementary Material: Contains the information obtained to fractals constructed with 7-mers, divided in three subfolders: 01 K-mer nucleotide appearance frequency and composition: contains 16 folders with the name of each species. The folders contain two files: a graphic representation of the 7-mers frequency in a .png format and a .txt file with the detailed 7-mers nucleotide content. 02 Fractal_7-mer: contains 16 .png files with the graphic representation of the fractals generated for each PRKN gene primates sequences, with the quadrants arrangement proposed in the methodology: upper, Cytosine-Adenine; lower, Thymine-Guanine; and the "Frequency Chaos Game Representation" methodology. The graphics are labeled with the species name. 03 Landscape 3D fractal: contains 16 .png files with the graphical representation of landscape 3D fractals constructed with the 7-mers. The graphics are labeled with the name of the primates species. 04 Supplementary Material: Contains 16 .png files that correspond to the fractals images generated with the Chaos Game Representation (CGR) algorithm, for the primates PRKN gene sequences, with 7-mers to corroborate the fractals generated with the FCGR methodology and the quadrants arrangement proposed. The files are labeled with the name of the species. 05 Supplementary Material: Contains two files: a .png named “Entropy_primate_species” that corresponds to the graphical representation of the primates species’ Shannon entropy; and an Excel file named “Shannon_entropy_Primate_species” that corresponds to a table with the individual Shannon entropy for the primates species. 06 Supplementary Material: Contains two .png files labeled “Dendrogram_Cophenetic_horizontal.png” and "Dendogram_7-mers_out.png" that correspond to the dendrograms constructed to PRKN gene, with a size of 7-mers, without and with the outgroup respectively.# 补充材料 01号补充材料：内含一个名为"灵长类PRKN基因核苷酸总频率与相对频率"的Excel文件，收录各物种的核苷酸总频率与相对频率数据。此外，各核苷酸的相对频率与总频率已以柱状图形式可视化，分别存放在两个独立子文件夹中，子文件夹分别命名为"01 PRKN核苷酸相对频率"与"02 PRKN核苷酸总频率"，文件夹内文件均以对应物种名称命名。 02号补充材料：内含针对16条灵长类PRKN基因序列生成的分形可视化结果。相关图形存放在16个子文件夹中，每个子文件夹以对应灵长类的学名命名。每个子文件夹内含9张图像，分别对应k值为3至11的k-mer，均通过频率混沌游戏表示（Frequency Chaos Game Representation, FCGR）方法生成。图像命名格式为物种名称+字母"k"+对应k-mer数值。同理，分形构建的象限排布顺序为：上象限——鸟嘌呤（G）-胸腺嘧啶（T），下象限——胞嘧啶（C）-腺嘌呤（A）。 03号补充材料：内含基于7-mer构建的分形相关信息，分为三个子文件夹： 01 k-mer核苷酸出现频率与组成：内含16个以物种名称命名的文件夹。每个文件夹包含两类文件：一是以.png格式存储的7-mer频率可视化图，二是收录7-mer核苷酸详细含量的.txt文件。 02 Fractal_7-mer：内含16个.png文件，为各灵长类PRKN基因序列生成的分形可视化结果，采用该方法指定的象限排布：上象限——胞嘧啶（C）-腺嘌呤（A）；下象限——胸腺嘧啶（T）-鸟嘌呤（G），且通过频率混沌游戏表示（FCGR）方法生成，图像以对应物种名称命名。 03 三维分形景观：内含16个.png文件，为基于7-mer构建的三维分形景观可视化结果，图像以对应灵长类物种名称命名。 04号补充材料：内含16个.png文件，均为基于混沌游戏表示（Chaos Game Representation, CGR）算法生成的灵长类PRKN基因序列分形图像，采用7-mer参数，用于验证通过FCGR方法及指定象限排布生成的分形结果。文件均以对应物种名称命名。 05号补充材料：内含两类文件：一是名为"Entropy_primate_species"的.png文件，为各灵长类物种的香农熵可视化结果；二是名为"Shannon_entropy_Primate_species"的Excel文件，收录各灵长类物种的单独香农熵数据表。 06号补充材料：内含两个.png文件，分别为"Dendrogram_Cophenetic_horizontal.png"与"Dendogram_7-mers_out.png"，对应基于PRKN基因构建的树状图，分别采用7-mer参数，其一不含外类群，其二包含外类群。