Hi everyone - I have a large dataset of aligned single-genome analysis (SGA) amino acid sequences from multiple species, tissues, and timepoints.
I would like to visualize the differences among them qualitatively and quantitatively (mutation frequency for example).
I tried Highlighter and SeqPublish from https://www.hiv.lanl.gov/, but any other cool ideas on software or program to use?
Thank you in advance for your help!
Programs BOXSHADE and TEXSHADE can be used to highlight AAs in alignments in various ways. Fig.6 in this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145222/) uses a technique were mutations are clustered into correlated networks. Creating a tree, perhaps circular, above your alignment is another intuitive way of comparing individual sequences. Trees make it more obvious if sequences belong to larger clusters.
http://ftp.cvut.cz/tex-archive/macros/latex/contrib/texshade/texshade.pdf
http://embnet.vital-it.ch/software/BOX_form.html
WebLogo (http://genome.cshlp.org/content/14/6/1188.long) is a tool that calculates the entropy within a multiple sequence alignment and then generates a visualization. The number and height of different letters in the chart infers diversity. Alternatively, you could just take the entropy values that are generated and construct a new figure in Excel.
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