Phylorgs

Copyright © Guillaume Louvel 2016-2023

Suite of tools for genomics & phylogeny, implemented during my PhD.

Related publication:

• Factors influencing the accuracy and precision in dating single gene trees, Guillaume Louvel, Hugues Roest Crollius. bioRxiv 2020.08.24.264671 (preprint); doi: https://doi.org/10.1101/2020.08.24.264671

Main modules

• dendro: manipulating trees (uses Ete3 and LibsDyogen);
• seqtools: manipulating sequences/alignments (uses Biopython);
• datasci: data analysis and plots;
• ensembltools, genomicustools: utils specific to the given data source;
• genchron: gene dating project, including snakemake pipelines;
• duprates: duplication rates project.

Visualisation tools

• genetree_drawer.py: draw reconciled gene trees;
• seqtools/printal.py: print alignments to terminal with colors (by codon/nucl/aa);
• seqtools/plot_al_conservation.py: plot alignment with column stats, and side tree;
• datasci.graphs.plottree: function for plotting trees with matplotlib.
• dendro/interactree.py: simple wrapper around Ete3 show commands;

Special dependencies

• LibsDyogen_py3
• ToolsDyogen_py3
• evosite3D
• fluidcondor

Optional dependency: atavistic-doc-tools

Required executables

for genchron

• PAML 4 codeml
• Newick utilities
• Beast2

for duprates

• phylobayes 4.1 or phylobayes MPI
• ALE
• Generax