/panphylo

Construction phylogenetic tree using genome or amino acid sequences

panphylo: Construction phylogenetic tree using genome or amino acid sequences

  1. core gene alignment and snp calling using snp-sites.

  2. mash distance and upgma tree.

  3. cgMLST using PubMLST scheme to generate distance matrix, splittree for Neighbor-Net phylogenetic network.

  4. orthofinder to infer species tree.