Comparative Genomics & Evolution — Hands-on

Gain expertise in comparative genomics and evolutionary relationships—from orthology inference and synteny to whole-genome alignment, pan-genomes, and selection tests.

Comparative Genomics & Evolutionary Relationships

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Session Index

Session 1 — Orthology, Paralogy & Synteny Session 2 — Whole-Genome Alignments & Pan-genomes Session 3 — Selection Tests, dN/dS & Conservation Session 4 — Mini Capstone: CompGen Pipeline

Session 1

Fee: Rs 6300

Orthology, Paralogy & Synteny

Homology concepts: orthologs vs paralogs; synteny blocks

Theory

Orthogroup inference & clustering at scale

OrthoFinder OrthoMCL MMseqs2

Synteny detection & visualization

MCScanX MUMmer Circos

Session 2

Fee: Rs 8400

Whole-Genome Alignments & Pan-genomes

Pairwise & multi-genome alignment strategies

minimap2 progressiveMauve LAST

Pan-genome construction, core/dispensable genes & ANI/AAI

Roary Panaroo pyANI

Structural variants & rearrangements across genomes

SyRI svanalyzer

Session 3

Fee: Rs 11200

Selection Tests, dN/dS & Conservation

Codon alignment & synonymous/nonsynonymous rates (dN/dS)

PAL2NAL codeml (PAML) HyPhy

Conservation scoring & constraint metrics across clades

phastCons phyloP MSA-based stats

Gene gain/loss & duplication events on species trees

CAFE ETE Toolkit

Session 4

Fee: Rs 14000

Mini Capstone: Comparative Genomics Pipeline

Design end-to-end comparative analysis & evaluation plan

Theory

Automate orthology→alignment→pan-genome with QC reports

Snakemake Conda/Mamba MultiQC

Deliver figures: synteny plots, pan-genome curves & selection tables

pandas matplotlib JupyterLab

PDF

Comparative Genomics & Evolutionary Relationships Training | Orthology, Synteny, WGA, Pan-genomes, dN/dS

Comparative Genomics & Evolution — Hands-on