I would like to visualize a large ("large" as in 20 bacterial genomes) multi-sequence alignment such that
(a) the sequences are wrapped within pages,
(b) the individual nucleotide letters remain visible (at least minutely), and
(c) nucleotide differences compared to a consensus are highlighted.
I wish to convert these alignments into PDF documents for subsequent printing.
Popular alignment viewers such as
Geneious have their difficulties with such alignment visualizations.
AliView cannot provide a wrapped layout, whereas
Geneious hangs for large alignments (24 GB RAM insufficient for alignment of 20 bacterial genomes).
Do you have any software suggestions?
Note: One option may be to use a console-based alignment viewer (such as alan or alv), if the resulting visualizations could be passed to cups-pdf.
Edit 1: The R-package msa has been among my earlier tryouts. While a wonderful tool for generating small, publication-ready visualizations, it too stalls once the alignment becomes too large. For example, an alignment of 20 bacterial genomes is not converted within two hours of executing command
myFirstAlignment <- msa(mySequences). Given that
msa essentially wraps texshade, I would guess that the processing time with
texshade would not be much smaller either.