An alignment and its tree

You have an alignment (FASTA with every record the same length) and, if you like, a tree of the same samples (Newick).

karyon --msa aln.fasta --with-tree tree.nwk -o alignment.svg

Each row is a sample, in the order of the tree's tips. A cell is coloured where the sample differs from the consensus, and the key names the colours. An alignment needs no place: it is drawn over all its columns.

Change it

To	Write
Only the columns that vary	--snps aln.fasta --with-tree tree.nwk
Every base, not only the differences	--style all after the alignment
Compare with one sample	--compare-to S01
Add what you know about each sample	--traits samples.tsv --columns lineage
Zoom into columns 100 to 160	aln.fasta:100-160 --msa aln.fasta --with-tree tree.nwk

The example files: aln.fasta, tree.nwk and samples.tsv. Every option: karyon help msa, or the command line reference. In Rust, it is a few lines.