mview
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desmid
MView extracts and reformats the results of a sequence database search or multiple alignment.
Hi there, believe this is where a new [D_IUPAC] groupmap would go! All the best, -Tim
I am trying to visualize the MSA of genes that are coding in two separate positons. I would be happy if I could display the amino acid sequence of one...
Is it possible to show only the nonconserved residues of the sequence alignment with the exception of the reference sequence (mostly the first one)? All conserved residues could than be...
Currently, only two different group maps are available for nucleotides: `D1` and `CYS`. `D1` contains conserved ring types only. In contrast to the groupmap `D1`, the colomap `D1` contains all...
The other two modes '-hsp ranked' and '-hsp discrete' make sense. The third mode 'all' is a historical artifact and has long been deprecated in the manual. Remove.
The mechanism for removing duplicated tags in marked up sequences is inefficient. Develop unit tests and refine.
See also #8
Historically, all parsers are hand-crafted format by format and version by version, but use common parser layout and components to achieve this and produce a common parse tree. Replace with...
Groundwork for this had been laid in the rewrite of the Display packages (commit: #b32c748)
Annotation columns "labels" are switched off using -label0, -label1, etc. Replace with something like: -labeloff:all -labelon:row,id,desc or some other syntax using named columns.