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Overview

This chapter contains a manual on phylogenetic analysis

Instruction

language
IDE

To recreate any of the part of this manual please install:

wget https://github.com/iliapopov17/NGS-Handbook/raw/refs/heads/main/envs/qc.yaml

conda env create -f phylo.yaml

And of cource do not forget to activate the envinronment!

conda activate phylo
Warning

Disclaimer: when using ete3 on WSL it will crash with error if you try to render any kind of picture (unless you have tunned X11 forwarding). It is recommended to use Ubuntu or macOS for steps with ete3. Anyway there is always an alternative!

08 Tanglegram

In the Tanglegram folder there is guide how to make co-phylogeny plots using R by several ways: (1) manually creating it with ggtree; (2) easily creating small tanglegram with cophyloplot() function in ape and (3) creating large tanglegram with dendextend.

07 Visualization Pro

In the Visualization Pro folder there is guide how to make a 1st class publication ready quality tree visualization using ggtree in R. By the end of the guide the circular ML-tree annotated with tip-points, tip-labels and heatmaps is created. The ideas from the first lesson continue here.

06 Phylogenomics

In the Phylogenomics folder there is guide how to reconstruct phylogeny using more than just one gene with two examples of pipelines. The 1st is about using mitochondrial genes and manual work with data. The 2nd is about using proteomes and extracting single-copy orthologs with Proteinortho. The main concern in phylogenomics studies is storing the data and naming the sequences properly. This manual pays a lot attention to it and provides insights on using BBMap to achieve this goal.

05 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.

04 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.

03 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).

02 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).

01 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).