-cssallows colouring of alignments using Cascading Style Sheets for more control and visual impact [example]. Style sheets can be exported and imported.
-gapcolorgive more control of HTML markup. Options
-coloring groupcolours residues according to a consensus threshold like the older
-coloring consensusmode, but uses the colour scheme of the chosen consensus group definitions rather than that of the residues themselves.
-dnaswitches on DNA/RNA alignment colouring and consensus group schemes instead of protein.
-con_gaps mode. Consensus colouring and consensus line computations normally count gap characters, so that sections of the alignment may be uncoloured and the consensus line reduced to gaps where the non-gap count falls below the threshold. Setting
-con_gaps offprevents this, allowing sequence-only based consensus thresholding.
-hsp methodallows control of the HSPs (NCBI BLAST 1.4) or gapped alignments (WU-BLAST 2.0, NCBI BLAST 2.0) used to construct alignment rows. Three processing methods are available with the : (1) 'ranked' [default] selects only the fragment(s) that are reflected in the search ranking; (2) 'all' fragments are selected for tiling; (3) 'discrete' selects all fragments, but allocates a separate alignment row for each. Per BLAST program details of this are available.
As of MView release 1.40, the code requires a minimum of perl version 5.004 and has been tested with 5.004_03/04 and 5.005_02. However, if you only have perl 5.003, you can run older versions of MView, also available from the ftp site.
Formatting and colouring of HTML alignments requires a fixed-width font (eg., Courier) and support for the <FONT> tag, so a recent version of a browser such as Netscape is recommended. In particular, use of style sheets as of MView release 1.40 requires that your browser supports HTML 4.0.
Brown, N.P., Leroy C., Sander C. (1998). MView: A Web compatible database search or multiple alignment viewer. Bioinformatics. 14(4):380-381. HTML MEDLINE