Comparing orthologies analysis

Manuscript: "Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes" Authors: E.S. Deutekom, B. Snel, T.J.P. van Dam

Disclaimer

This serves to share code and data for reproducibility. Due to the amount of data, only the files in green in the flowchart are provided. The flowchart shows a summary of the workflow, with the most important scripts and files. Some scripts that are used for supplementary figures and/or results are not shown. Any additional data can be shared upon request.

Contained directories and files

Manuscript figures: Manuscript_Plots.ipynb

Supplementary figures: Supplementary Material Figures.ipynb

eukarya directory

Contains part of the data and scripts used in the analyses minimally needed to reproduce the figures.

Software and tools in analyses

• blastp 2.7.1
• hhmbuild HMMER 3.1b2
• python 3.7.6
• samtools 0.1.19-96b5f2294a

Python packages

• ete3 3.1.1
• biopython 1.76
• numpy 1.18.1
• pandas 1.0.1
• scipy 1.4.1

Figures directory

Contains the (supplementary) figures prduced for the manuscript. Figures were produced using the following list of software and tools.

Software and tools

• python 3.7.6

Python packages

• matplotlib 3.1.0
• pandas 0.24.2
• numpy 1.16.4
• scipy 1.3.0
• seaborn 0.10.0
• snakemake 5.5.4