Repository for Phylogenetics Course Guides in Bioinformatics Institute

This repository for Phylogenetics Course Guides in Bioinformatics Institute 2023-2024
It can be used as a helpful repository with all possible cheat-sheets for phylogenetic studies

Rooting and comparing trees & Dating

In the Root Date folder there is guide how to root trees using different approaches (by a known external clade / midpoint rooting / non-reversible model), how to compare these approaches and how to perform root-supporte tree visualisation (rootstrap). Also there is a mini-project on dating the common ancestor of smoky leopards with "full-circle" study: downloading the data from NCBI using efetch, aligning the sequences with mafft, trimming with trimal and tree construnction with iqtree2 followed by visualization and analysis in GUI apps: Beauti, Tracer, TreeAnnotator and FigTree.

Preparing the alignment and building trees

In the Trees folder there is guide how to prepare the alignment by cutting bad areas out of with trimAl, how to select the model with ModelTest-NG and ModelFinder, how to perform a tree search with RaxML-NG and IQ-TREE and how to do topology assesment with bootstrap.

Multiple sequence alignment

In the MSA folder there is guide how to perform multiple sequence alignment using all possible tools (clustalw, clustalo muscle, mafft, kalign, tcoffee, prank).

Working with NCBI

In the Mining data folder there is guide how to work with NCBI using all possible ways - R (reutils), Python (Bio::Entrez) and bash (esearch).

Drawing Trees

In the Intro Trees folder there is guide how to draw phylogenetic trees using both R (ape, ggtree) and Python (Bio::Phylo, ete3).