Comparative Genomics and Phylogenetic Analysis in KBase

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KBase’s comparative genomics and phylogenetic analysis tools enable researchers to understand evolutionary relationships between organisms and explore structural and functional variance across genomes. By integrating public datasets with user data and tools to search for sequence homology, explore gene orthology, and construct phylogenetic linkages between organisms, KBase provides an advanced and useful platform for comparative genomics research.

KBase Comparative Genomics and Phylogenetic Analysis Capabilities

Phylogenetic Analysis

  • Reconstruct a phylogenetic tree based on conserved orthologous groups using Insert Genome into Species Tree
  • Examine functional content using View Function Profile for Genomes and View Function Profile Phylo
  • Compare proteomes and produce a synteny map dot plot matrix and table of gene differences with Compare Two Proteomes
  • View the pangenome in a phylogenetic context using Phylogenetic Pangenome Accumulation

Sequence Homology

  • Search and compare translated protein sequences via BLASTx, tBLASTn, and tBLASTx
  • Search and compare nucleotide sequences via BLASTn
  • Search and compare protein sequences via BLASTp and psiBLAST
  • Build and analyze multiple sequence alignments (MSA) for nucleotide or protein sequences via MUSCLE

Pangenome Exploration

  • Group orthologous protein sequences and identify core and non-core genes across multiple species using Build Pangenome with OrthoMCL
  • Build a pangenome and evaluate protein family conservation with Compute Pangenome
  • View a microbial pangenome as a circle plot using Pangenome Circle Plot
  • Compare isofunctional and homologous gene families within a pangenome with Compare Genomes from Pangenome