School of Bioinformatics · Microbial & evolutionary genomics
Phylogenetics & Molecular Evolution
Phylogenetic trees appear in papers on pathogens, gene families and biodiversity, and they are often over-interpreted. This course teaches how trees are built, what support values mean and how to draw defensible conclusions.
Course overview
Phylogenetics & Molecular Evolution covers how trees are inferred from sequences: identifying homologs, building and trimming multiple alignments, choosing a substitution model, and estimating distance-based and maximum-likelihood trees with measures of support.
Phylogenies are often read with more confidence than the data allow. The course gives equal weight to interpretation: what a bootstrap value does and does not mean, how rooting changes the story, and why a well-supported tree can still be wrong if the alignment or the model is poor.
Learning outcomes
By the end of the course you will be able to:
- Build multiple sequence alignments and assess their quality
- Choose substitution models with information criteria
- Infer distance and maximum-likelihood trees
- Interpret bootstrap and branch support without over-reading it
- Present annotated trees clearly with iTOL or ggtree
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- Bioinformatics Foundations or equivalent
Best suited to
- Microbiology, zoology and biotechnology students
- Researchers working on gene families or pathogen evolution
Module-wise syllabus
5 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- Orthologs and paralogs
- MAFFT and Clustal Omega
- Trimming alignments
Topics
- JC69, K80, HKY and GTR
- Rate heterogeneity (+Γ, +I)
- Model selection with AIC and BIC
Topics
- Neighbour-joining and UPGMA
- Maximum likelihood with IQ-TREE
- An introduction to Bayesian inference
Topics
- Bootstrap and ultrafast bootstrap
- Rooting and outgroups
- Common misreadings
Topics
- From sequences to an annotated tree
- Figure with iTOL
- Methods write-up
Practical sessions and projects
Capstone project
Trace a gene family
Collect homologous sequences, build and test a maximum-likelihood phylogeny and interpret it without reading more into it than the data support.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- Homology and alignment
Collect homologs of a globin gene with BLAST, align them with MAFFT and Clustal Omega, and trim the alignment with trimAl.
- Models of evolution
Compare substitution models for the same alignment with ModelFinder and justify the choice by AIC and BIC.
- Tree inference
Infer neighbour-joining and maximum-likelihood trees with IQ-TREE and compare their topologies.
- Support and interpretation
Compute standard and ultrafast bootstrap support, root the tree with an outgroup and identify clades that are over-interpreted.
- Project: a gene-family phylogeny
Build an annotated gene-family phylogeny, render it with iTOL and write the methods section.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- Globin gene family: Homolog collection and a gene-family tree.NCBI RefSeq and UniProt
- SARS-CoV-2 genome sequences: Alignment and tree building on closely related genomes.NCBI Virus
Core reading
- Minh BQ et al. (2020). IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Molecular Biology and Evolution 37:1530–1534.
- Katoh K, Standley DM (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30:772–780.
- Felsenstein J. Inferring Phylogenies. Sinauer Associates, 2004.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Phylogenetics & Molecular Evolution, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Phylogenetics & Molecular Evolution
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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