[FEAT] Phylogeny: multiple sequence alignment & tree

[jananiravi]

MSA

• add kalign3
• T-Coffee, Expresso, structure-based sequence alignment
• paralogs --> MSA

MSA + Tree

• leaf: AccNum appears twice in the name
• leaf: include domain architecture in the name as well? | not now!!
• msa: check subsetting criteria | why so few? show all?
• msa/tree: make sure the starting sequences are from the aln file
• generate tree from msa (not importing PDF)
• try the following packages:
  • ggtree
  • ggseqlogo
• add legend
• make sure custom outpath for fasta files works
  fasta --> msa --> pdf
  • check out other tex, pdf options!
  • check in firefox, chrome, safari -- PDF rendering or downloading?
• eventually, combine so as to have one tree per query
• add sunburst plots to phylogeny
• remove 'Press me to Zoom' for the tree tab, if it's going to PDF -- relevant for lineage plots?

Paralogs

• add MSA option for sets of paralogs | clickable
• clickable paralog table | brings up entries for the reported accnum

Additional notes

• It looks like the current msa generation function is this function https://github.com/JRaviLab/molevol_scripts/blob/main/R/msa.R#L32-L169
• Front-end function call: https://github.com/JRaviLab/molevolvr1.0/blob/main/app.R#L3123-L3173
• Uses https://www.rdocumentation.org/packages/msa/versions/1.4.3/topics/msa to align