GitHub

Comparative Genomics Workflows

This page documents comparative genomics workflows and functions in Mycelia.

Pangenome Construction

Build pangenomes representing variation across multiple genomes.

Functions

  • Core and accessory genome identification
  • Gene presence/absence analysis
  • Pangenome graph construction

Phylogenetic Analysis

Construct and analyze phylogenetic trees.

Functions

  • Distance matrix calculation
  • Tree building algorithms
  • Bootstrap analysis

Synteny Analysis

Identify conserved gene order and chromosomal rearrangements.

Functions

  • Colinear block detection
  • Synteny conservation metrics
  • Rearrangement identification

Pairwise Comparison

Compare two genomes to identify similarities and differences.

Functions

  • Genome alignment
  • SNP/indel detection
  • Structural variation analysis