Molecular Phylogenetics & Tree Reconstruction — Hands-on

Gain expertise in molecular phylogenetics—curation, model testing, ML/Bayesian tree building, bootstraps, clocks, dating, and publication-grade visualization.

Molecular Phylogenetics & Tree Reconstruction

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Session Index

Session 1 — Data Curation & Models Session 2 — ML/Bayesian Inference Session 3 — Clocks, Dating & Support Session 4 — Mini Capstone: Phylo Pipeline

Session 1

Fee: Rs 6300

Data Curation & Models

MSA curation, trimming & partitioning strategies

MAFFT MUSCLE trimAl

Nucleotide & amino-acid substitution models

JC69/K80/GTR WAG/JTT/LG

Model selection with information criteria & tests

ModelFinder ModelTest-NG AIC/BIC

Session 2

Fee: Rs 8400

ML/Bayesian Inference

Distance, ML and Bayesian tree building methods

FastTree RAxML-NG IQ-TREE 2 MrBayes

Support metrics: bootstraps, SH-aLRT & posterior probs

UFboot PP

Partitioned & mixture models; heterogeneous rates

Γ rates I+G C60

Session 3

Fee: Rs 11200

Clocks, Dating & Support

Strict vs relaxed molecular clocks & calibrations

BEAST 2 TreeTime Calibration priors

Divergence time estimation & credibility intervals

HPD ranges ESS checks

Topology tests & congruence across partitions

AU/SH tests Approximately unbiased

Session 4

Fee: Rs 14000

Mini Capstone: Phylo Pipeline

Design reproducible pipeline from MSA to dated tree

Theory

Automate inference & support metrics with reports

Snakemake Conda/Mamba MultiQC

Visualize & annotate trees for publication & iTOL

FigTree iTOL ETE/DendroPy

PDF

Molecular Phylogenetics & Tree Reconstruction Training | ML, Bayesian, Clocks & Dating

Molecular Phylogenetics & Tree Reconstruction — Hands-on