Technical interview guide

Phylogenetics & Evolutionary Analysis

Reconstructing evolutionary relationships from sequence data — tree-building methods, substitution models, and molecular clocks.

Read: 50 min
Practice MCQs: 25
Interview QA: 25
Edition: v3
Editorial status: Reviewed
Relevant for: Computational Biologist

Scope: MAFFT 7; current IQ-TREE, RAxML-NG, MrBayes and BEAST documentation; ModelFinder, ultrafast bootstrap, multispecies coalescent and recombination source literature reviewed 2026-09-04.

Interview QA

Treat each question like a live interview question: answer out loud first (structure, assumptions, tradeoffs), then open the model answer to spot gaps and rehearse a tighter follow-up.

Curated: 2026-10-05 · Written: 2026-10-05 · Reviewed: 2026-10-04

QA-1

Design and defend a phylogenetic analysis for homology and orthology.

QA-2

Design and defend a phylogenetic analysis for taxon sampling.

QA-3

Design and defend a phylogenetic analysis for multiple-sequence alignment.

QA-4

Design and defend a phylogenetic analysis for alignment uncertainty.

QA-5

Design and defend a phylogenetic analysis for substitution models.

QA-6

Design and defend a phylogenetic analysis for rate heterogeneity.

QA-7

Design and defend a phylogenetic analysis for partitions.

QA-8

Design and defend a phylogenetic analysis for maximum likelihood.

QA-9

Design and defend a phylogenetic analysis for tree search.

QA-10

Design and defend a phylogenetic analysis for parsimony.

QA-11

Design and defend a phylogenetic analysis for bootstrap support.

QA-12

Design and defend a phylogenetic analysis for Bayesian posterior.

QA-13

Design and defend a phylogenetic analysis for MCMC convergence.

QA-14

Design and defend a phylogenetic analysis for rooting.

QA-15

Design and defend a phylogenetic analysis for branch lengths.

QA-16

Design and defend a phylogenetic analysis for molecular clocks.

QA-17

How do you test hypotheses of continuous phenotypic trait evolution across a phylogeny, specifically contrasting Brownian Motion and Ornstein-Uhlenbeck models?

QA-18

Design and defend a phylogenetic analysis for gene and species trees.

QA-19

Design and defend a phylogenetic analysis for duplication and loss.

QA-20

Design and defend a phylogenetic analysis for incomplete lineage sorting.

QA-21

Design and defend a phylogenetic analysis for recombination.

QA-22

Design and defend a phylogenetic analysis for horizontal transfer.

QA-23

Design and defend a phylogenetic analysis for long-branch attraction.

QA-24

How do you design a scalable near-real-time Bayesian phylogenetics pipeline for genomic pathogen surveillance to infer transmission dynamics and divergence dates under molecular clock models?

QA-25