An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes

This repository contains sequence alignments, trees, and python scripts used for the paper: An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes Within Part_1: Constraint_alignments_and_domain_IDs: This dir contains the constraint trees, and the fastas necessary for the AU comparison Dating: This contains all files relevant for the dating analysis Expanded alignments: this contains the various concatenates for the slow vs. fast/ number of markers test (cat1 and cat4 refer to IQTREE rate categories, 1 is slow, 4 is fast) Python scripts: this includes the python scripts needed to calculate AB stem, check monophyly, convert IQTREE rate files into fasta, total tree length, and the python script to write constraint trees (from a simple .tsv) Result_files: this contains the .csvs with all the results used for the paper, as well as the trees from the model/marker tests Annotations_tables: contains the supplementary tables, sheets and scripts for the annotations, including table S1 in 7_Unimarkers_summary Part_2_main_marker_analyses contains: These are the data supplements for the analyes described in the second half of the paper,referring to the 'new' marker set constructed from multiple previous marker sets. Concatenations has the various concatenations and their component alignment fatsta files, and tree files associated with them Marker_analysis_Supp_scripts_tables has the various python/r/bash scripts used as well as the sheets and tables of results Supp_27,54,95 has the unaligned and aligned sequences after each round of 'pruning' as well as the treefiles.

本仓库收录了用于论文《基于古老垂直进化基因估算生命树最深分支》(An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes)的序列比对结果、系统发育树及Python脚本。
### Part_1: Constraint_alignments_and_domain_IDs
该目录包含约束树以及用于AU检验所需的FASTA格式文件。
### Dating:
该目录收录与年代分析相关的全部文件。
### Expanded alignments:
该目录包含用于“速率快慢与标记数量测试”的各类串联比对文件，其中cat1与cat4对应IQTREE的速率分类组，1代表慢速率类别，4代表快速率类别。
### Python scripts:
该目录包含所需的各类Python脚本，涵盖计算AB茎、检验单系性、将IQTREE速率文件转换为FASTA格式、计算总树长的脚本，以及用于从简单TSV文件生成约束树的脚本。
### Result_files:
该目录包含论文中使用的全部结果对应的CSV文件，以及模型与标记测试所得的系统发育树文件。
### Annotations_tables:
该目录包含用于注释分析的补充表格、工作表及脚本，其中包括7_Unimarkers_summary文件夹中的表S1。
### Part_2_main_marker_analyses
该部分包含论文后半部分所述分析的数据补充材料，对应从多个既往标记集构建的“新”标记集。
#### Concatenations:
该目录包含各类串联比对文件及其对应的组分比对FASTA文件，以及相关联的系统发育树文件。
#### Marker_analysis_Supp_scripts_tables:
该目录包含所用的各类Python、R及Bash脚本，以及结果对应的工作表与表格。
#### Supp_27,54,95:
该目录包含每一轮“修剪”步骤后的未比对与已比对序列，以及对应的系统发育树文件。