Tregwiki:Multi-sequence visualization of features

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Revision as of 18:28, 9 December 2007 by Bill Flanagan (Talk | contribs)
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There is really no good tool for this yet that I know of. I've tried some but never really found what I wanted, two or more sequences with features plotted on them or display something like a synteny-plot:

    • Alfresco
    • ACT
    • self-written tools that operate in text-mode (ugly, e.g. emboss' prettyseq)
    • Apollo (also in synteny mode)
    • Vector NTI in aligment mode ("Show all features")
    • My MUMU-tools (export to svg)
    • gff2ps (only one sequence?)
    • Multipipmaker and Vista, when in doubt use multipipmaker, Vista comes almost without any documentation and uses a strange "plotfile" format
    • feature_draw from bioperl (though only for one sequence at a time, very configurable)
    • Argo whole genome viewer/editor, with comparative view
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