How to build a phylogenetic tree for a gene family – step by step | Gene Family Analysis Ep. 1

How to build a phylogenetic tree for a gene family – step by step (MEGA 12 + FigTree) | Gene Family Analysis Ep. 1 In this episode you will build a publication-ready phylogenetic tree from raw protein sequences, using free software and a real example: 21 alkaline/neutral invertases from Arabidopsis, rice and Citrus. You will learn: • what phylogeny is, and how to read a tree (tips, nodes, branches, clades, root, bootstrap) • orthologs vs paralogs • how to align sequences with MUSCLE in MEGA 12 • how to choose the best substitution model (BIC) • how to build a maximum likelihood tree with bootstrap support • how to export it and style it in FigTree • the 6 mistakes reviewers notice, and a methods paragraph you can adapt Chapters 0:00 Why every gene family paper has a tree 1:51 What is phylogeny? 2:31 Anatomy of a phylogenetic tree 3:08 Orthologs vs paralogs 4:25 Today's plan 4:49 Part 1 – Prepare your sequences 6:15 Real example: 21 alkaline/neutral invertases 7:19 Multiple alignment with MUSCLE (MEGA 12) 8:45 Part 2 – Find the best substitution model 10:01 Maximum likelihood tree settings 11:43 Neighbor-joining vs maximum likelihood 12:40 Part 3 – Export the Newick tree 13:18 Style the tree in FigTree 14:01 How to read the final tree 15:02 Part 4 – 6 common mistakes 15:49 Methods paragraph for your paper 16:21 Next episode Software (free): MEGA 12 · MUSCLE · FigTree v1.4.4 Next episode: gene structure and conserved motifs (GSDS + MEME), aligned with today's tree. #phylogenetics #bioinformatics #genefamily #MEGA #FigTree #molecularbiology #plantscience