Fig. 1
From: EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets
EasyCGTree flowchart. Note: The algorithm uses FASTA/multi-FASTA formatted amino acid sequences from prokaryotic genomes (i.e., proteome) as input data. EasyCGTree includes the supermatrix (SM) and supertree (ST) approaches to infer phylogeny. Several profile HMMs of core gene sets have been prepared in advance to construct a profile HMM database (PHD) that is enclosed in the package and used for homolog searching. Customized gene sets can also be used to build profile HMMs and added to the PHD