User interface tools for bioinformatics.
36 Stars
Updated Last
5 Months Ago
Started In
February 2020



Build Status

This package provides plotting functions for protein structures, multiple sequence alignments, and some other related plots like protein structure contact maps.

So far, plotting methods exist for packages:

  • BioStructures.jl
  • MIToS.jl
  • FastaIO.jl
  • FASTX.jl

Plotting methods in development:

  • MolecularGraph.jl
  • ProtoSyn.jl


Enter the package mode by pressing ] and run add BioMakie.


The main plotting functions are plotstruc and plotmsa, along with their mutating versions, plotstruc! and plotmsa!. The mutating functions allow the user to add multiple plots to the same Figure, using grid positions.

using BioMakie
using GLMakie
using BioStructures
struc = retrievepdb("2vb1") |> Observable
## or
struc = read("2vb1.pdb", BioStructures.PDB) |> Observable

fig = Figure()
plotstruc!(fig, struc; plottype = :ballandstick, gridposition = (1,1), atomcolors = aquacolors)
plotstruc!(fig, struc; plottype = :covalent, gridposition = (1,2))

To view a multiple sequence alignment, use the plotmsa function with a Pfam MSA or fasta file.

using FASTX
reader = open(FASTX.FASTA.Reader, "PF00062_full.fasta")
msa = [reader...] |> Observable
## or 
using MIToS
using MIToS.MSA
msa ="", Stockholm)

fig = plotmsa(msa; colorscheme = :tableau_blue_green)

Additional examples

Alpha shapes can be used to visualize the surface of a protein structure