Protein and DNA alignments for ILS and Entropy calculations

Data and results for reproducing the Entropy and ILS calculations described in "Assessing the potential of ancient protein sequences in the study of hominid evolution" (https://doi.org/10.1093/gbe/evag035). The data present here include the Protein, Exon and Intron and Exon only alignments for 12 enamel and bone proteins (AHSG, ALB, AMBN, AMELX, AMELY, AMTN, COL17A1, ENAM, MMP20, ODAM, COL1A1, COL1A2). In detail, two main folders are found here: a) Intro_Exon_Protein_Entropies_and_Alignments (with 3 subfolders) ~ Corresponds to "Informational content: exons, introns and proteins" section of methods Homind_Data_Type_Entropy_Raw_Data. Contains all the raw fasta files in 3 subfolders, one for each data type: amino acids, exons-and-intons and exons-only. Each of the 3 subfolders contains the fasta sequences for multiple individuals from each of the following 4 hominid species: Homo sapiens, Pan troglodytes, Gorilla gorilla, Pongo abelii. Homind_Data_Type_Entropy_ALIGNMENTS. Contains 3 fasta files for each of the 12 enamel and bone proteins-genes. Each of the 3 fasta files contains the alignment sequences of 4 hominid species (Homo sapiens, Pan troglodytes, Gorilla gorilla, Pongo abelii) of a specific data type: amino acids, exons-and-intons and exons-only. Additional files include the Calc_Entropy_of_Fasta_IEP.r R script, which can be used to calculate the entropy of an alignment and the Calc_Entropy_Introns_Exons_Proteins.sh bash files, which can be executed to automatically run the R script over all 12 genes. Entropy_Measurements. Contains 3 fasta files for each of the 12 enamel and bone proteins-genes. Each of the 3 fasta files contains the entropy score generated from the alignment of sequences of 4 hominid species (Homo sapiens, Pan troglodytes, Gorilla gorilla, Pongo abelii) of a specific data type: amino acids, exons-and-intons and exons-only. b) DNA_vs_Protein_Alignments (2 subfolders) ~ Corresponds to "Incomplete lineage sorting, DNA and proteins" section of methods DNA_Data_Hominid_Reference_Alignments. Contains 1 folder (GENE_TREES_ENAMEL) with the results of running a phylogenetic analysis on the DNA gene alignments each of the 4 hominid species (Homo sapiens, Pan troglodytes, Gorilla gorilla, Pongo abelii) and each of the 12 enamel and bone genes. Additonally the R script Tree_Dist.r can be used to compare the generated phylogenetic trees with a model reference tree (Hominid_Tree.txt) for these 4 species. Protein_Data_Hominid_Reference_Alignments. Contains 12 folders, one for each gene, with the phylogenetic results of the protein sequences of the 4 hominid species (Homo sapiens, Pan troglodytes, Gorilla gorilla, Pongo abelii). The phhylogenetic trees can be re-generated using the Generate_Trees_PhyML.sh bash script. Additonally the R script Tree_Dist.r can be used to compare the generated phylogenetic trees with a model reference tree (Hominid_Tree.txt) for these 4 species. The python script Topology_Per_Gene.py can be used to generate the main component of Figure 2 of the main text. c) Protein_Entropy_Workflow (multiple subfolders) ~ Corresponds to "Entropy and evolutionary conservation rates" section of methods A third folder is also present. This folder contains the workflow for the more in-depth entropy and evolutionary rates calculations of the 12 enamel and collagen proteins.The difference between these calculations and the ones of a) Homind_Data_Type_Entropy_Raw_Data is that here, the calculations are berformed over dozens of individuals for each species instead of a single representative. While there are multiple subfolders here, the most important on is the Snakefile described below. Snakefile. This file is a Snakemake script which can automatically reproduce the analysis and the results plotted in Figure 3 of the corresponding manuscript. This file can be execute with '' snakemake -j8 -F '', provided that snakemake is installed on your machine. NOTE ON PREREQUISITES While a number of scripts need only a few prerequisites and can be run on any computer (e.g. R script or python scripts), I recommend using a conda environment on a Linux machine, which would allow the user to execute any file provided here. Conda users can easily access all prerequisites for running these files using '' conda create -n Entropy -c conda-forge -c bioconda biopython r-bio3d snakemake biopython '' and activating the created "Entropy" conda environment.本数据集用于复现《Assessing the potential of ancient protein sequences in the study of hominid evolution》（DOI: 10.1093/gbe/evag035）中提及的熵与不完全谱系分选(Incomplete lineage sorting, ILS)相关计算。 本次提供的数据包含12种釉质与骨骼蛋白（AHSG、ALB、AMBN、AMELX、AMELY、AMTN、COL17A1、ENAM、MMP20、ODAM、COL1A1、COL1A2）的蛋白、外显子-内含子及仅外显子序列比对结果。 本次数据集包含三个主要文件夹： a) Intro_Exon_Protein_Entropies_and_Alignments（含3个子文件夹）——对应方法部分的「信息含量：外显子、内含子与蛋白」章节 1. Homind_Data_Type_Entropy_Raw_Data：包含3个子文件夹下的所有原始FASTA文件，分别对应三种数据类型：氨基酸序列、外显子-内含子序列以及仅外显子序列。三个子文件夹各自存储了以下4种人科物种的多个个体的FASTA序列：智人(Homo sapiens)、黑猩猩(Pan troglodytes)、西部大猩猩(Gorilla gorilla)、婆罗洲猩猩(Pongo abelii)。 2. Homind_Data_Type_Entropy_ALIGNMENTS：为12种釉质与骨骼蛋白-基因各提供3个FASTA文件。每个FASTA文件包含对应数据类型（氨基酸序列、外显子-内含子序列、仅外显子序列）的4种人科物种的比对序列。额外附带的文件包括：用于计算比对序列熵的R脚本Calc_Entropy_of_Fasta_IEP.r，以及可批量运行该R脚本以处理全部12个基因的Bash脚本Calc_Entropy_Introns_Exons_Proteins.sh。 3. Entropy_Measurements：为12种釉质与骨骼蛋白-基因各提供3个FASTA文件。每个FASTA文件存储了对应数据类型（氨基酸序列、外显子-内含子序列、仅外显子序列）的4种人科物种序列比对所生成的熵分值。 b) DNA_vs_Protein_Alignments（含2个子文件夹）——对应方法部分的「不完全谱系分选、DNA与蛋白」章节 1. DNA_Data_Hominid_Reference_Alignments：包含一个名为GENE_TREES_ENAMEL的文件夹，存储了对4种人科物种的12种釉质相关蛋白基因的DNA序列比对结果进行系统发育分析得到的结果。此外附带R脚本Tree_Dist.r，可用于将生成的系统发育树与对应4个物种的模型参考树Hominid_Tree.txt进行比对。 2. Protein_Data_Hominid_Reference_Alignments：包含12个文件夹，每个对应一个基因，存储了4种人科物种的蛋白序列的系统发育分析结果。可通过Bash脚本Generate_Trees_PhyML.sh重新生成系统发育树。此外，R脚本Tree_Dist.r可用于将生成的系统发育树与模型参考树Hominid_Tree.txt进行比对；Python脚本Topology_Per_Gene.py可用于生成正文图2的核心内容。 c) Protein_Entropy_Workflow（含多个子文件夹）——对应方法部分的「熵与进化保守率」章节 本文件夹包含针对12种釉质与胶原蛋白蛋白的更深入熵与进化速率计算的工作流。与a)部分的Homind_Data_Type_Entropy_Raw_Data计算不同，本部分针对每个物种的数十个个体进行计算，而非仅单个代表个体。尽管包含多个子文件夹，但核心文件为如下所述的Snakemake脚本。 Snakefile：该文件为Snakemake脚本，可自动复现对应手稿中图3的分析与结果。若本地已安装Snakemake，可通过命令"snakemake -j8 -F"执行该脚本。 前置条件说明 部分脚本仅需少量依赖，可在任意计算机上运行（如R脚本或Python脚本），但推荐在Linux机器上使用Conda环境，以支持本数据集提供的所有文件的运行。Conda用户可通过以下命令创建名为Entropy的环境并安装所有依赖："conda create -n Entropy -c conda-forge -c bioconda biopython r-bio3d snakemake biopython"，随后激活该环境即可。