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
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
.
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
.
In the MSA folder there is guide how to perform multiple sequence alignment using all possible tools (clustalw
, clustalo
muscle
, mafft
, kalign
, tcoffee
, prank
).
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
).
In the Intro Trees folder there is guide how to draw phylogenetic trees using both R
(ape
, ggtree
) and Python
(Bio::Phylo
, ete3
).