Algorithm Architecture & Decision Matrices
Detailed comparison cards highlighting algorithmic trade-offs, strengths, weaknesses, and recommended production setups.
Primary Software & Algorithms in Population Genetics & Phylogenetics
Direct command-line recipes, Conda environment specifications, memory footprints, and license metadata.
Efficient and versatile phylogenomic software with ultrafast bootstrap approximation (UFBoot2), automated substitution model selection (ModelFinder), and ancestral state reconstruction.
conda install -c bioconda iqtree
Fast and scalable maximum-likelihood phylogenetic tree inference tool designed for massive phylogenomic datasets, handling thousands of concatenated genes across hundreds of taxa.
conda install -c bioconda raxml-ng
High-accuracy comparative genomics platform for orthogroup inference, gene duplication event dating, gene tree-species tree reconciliation, and rooted species tree estimation.
conda install -c bioconda orthofinder
Bayesian evolutionary analysis sampling trees using Markov chain Monte Carlo (MCMC). Estimates rooted time-measured phylogenies, strict and relaxed molecular clock rates, and demographic history.
conda install -c bioconda beast2
Infers approximately-maximum-likelihood phylogenetic trees from huge alignments of nucleotide or protein sequences (up to millions of taxa) in minutes rather than days.
conda install -c bioconda fasttree
Grammar of graphics framework for visualizing and annotating phylogenetic trees with complex genomic data, trait matrices, multiple sequence alignments, and ancestral node states.
R -e 'BiocManager::install("ggtree")'
Proceed to Stage 11: Long-Read Sequencing (PacBio & ONT)
Sequencing pipelines proceed sequentially. Move forward to the next analytical domain to explore downstream algorithms and execution profiles.