I have a tab-delimited file (instead of a standard
fasta input), which is a pre-aligned MSA (the first column is the accession number/leaf name for the alignment/tree, and the second column is the alignment, e.g., the output of Kalign). I would like to use one of the existing functions or tweak an existing function within
msa to visualize my existing alignments using msaPrettyPrint (or something similar) instead of generating new ones each time with the fasta file & msa.
In summary, please let me know if any of you have suggestions for:
1) displaying pre-aligned sequences in any compatible format
2) is there a way to read a
tsv and specify the
leaf vs. the
alignment. I could convert the files to fasta, but this might be a helpful feature.
kalign as one of the alignment algorithms since this works better to align several 100 protein sequences better than
PS. @ulrich.bodenhofer thanks for the great package to generate MSA+tree!