phylogenetics

name	phylogenetics
description	Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.
license	Unknown
tags	["scientific-skills","phylogenetics","cheminformatics","machine-learning","bioinformatics"]
metadata	{"skill-author":"Kuan-lin Huang"}

-|-------------|---------| | GTR+G4 | General Time Reversible + Gamma | Most flexible DNA model | | HKY+G4 | Hasegawa-Kishino-Yano + Gamma | Two-rate model (common) | | TrN+G4 | Tamura-Nei | Unequal transitions | | JC | Jukes-Cantor | Simplest; all rates equal |

Protein Models

Model	Description	Use case
LG+G4	Le-Gascuel + Gamma	Best average protein model
WAG+G4	Whelan-Goldman	Widely used
JTT+G4	Jones-Taylor-Thornton	Classical model
Q.pfam+G4	pfam-trained	For Pfam-like protein families
Q.bird+G4	Bird-specific	Vertebrate proteins

Tip: Use -m TEST to let IQ-TREE automatically select the best model.

Best Practices

• Alignment quality first: Poor alignment → unreliable trees; check alignment manually
• Use linsi for small (<200 seq), fftns or auto for large alignments
• Model selection: Always use -m TEST for IQ-TREE unless you have a specific reason
• Bootstrap: Use ≥1000 ultrafast bootstraps (-B 1000) for branch support
• Root the tree: Unrooted trees can be misleading; use outgroup or midpoint rooting
• FastTree for >5000 sequences: IQ-TREE becomes slow; FastTree is 10–100× faster
• Trim long alignments: TrimAl removes unreliable columns; improves tree accuracy
• Check for recombination in viral/bacterial sequences before building trees (RDP4, GARD)

Additional Resources

• MAFFT: https://mafft.cbrc.jp/alignment/software/
• IQ-TREE 2: http://www.iqtree.org/ | Tutorial: https://www.iqtree.org/workshop/molevol2022
• FastTree: http://www.microbesonline.org/fasttree/
• ETE3: http://etetoolkit.org/
• FigTree (GUI visualization): https://tree.bio.ed.ac.uk/software/figtree/
• iTOL (web visualization): https://itol.embl.de/
• MUSCLE (alternative aligner): https://www.drive5.com/muscle/
• TrimAl (alignment trimming): https://vicfero.github.io/trimal/