Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the applet parameters and other documentation in the links to the left.
<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"uniref50.fa" , "treeFile":"ferredoxin.nw" , "userDefinedColour":"C=yellow; R,K,H=FF5555; D,E=5555FF" , "showFullId":"false" , "sortByTree":"True" , "showSequenceLogo":"true" , "showGroupConsensus":"true"} prots=true /> | User Defined Colours, loads an associated Newick format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment. |
<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions", "file":"uniref50.fa" , "features":"exampleFeatures.txt" , "showFeatureSettings":"true" , "wrap":"true" , "showAnnotation":"false" , "windowHeight":"500" , "windowWidth":"650" , "showFullId":"false"}/> | Displays a features file on the alignment |
<@jvlitebutton appjar="${content.jvl},${content.jmol}" params={ "permissions":"all-permissions" , "file":"uniref50.fa" , "defaultColour":"Strand Propensity" , "wrap":"true" , "showAnnotation":"false" , "windowHeight":"500" , "windowWidth":"650" , "showFullId":"false" , "PDBfile":"1gaq.txt FER1_MAIZE"} /> | Associates PDB file 1GAQ with sequence FER1_MAIZE |
<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"jpred_msa.fasta" , "jnetfile":"jpred_msa.seq.concise" , "defaultColour":"Clustal" , "showAnnotation":"true" , "windowHeight":"515" , "windowWidth":"650" , "showConservation":"false" , "showQuality":"false" , "showConsensus":"false" , "showFullId":"false"} /> | Displays a Multiple Sequence Alignment Based JNet Prediction for a Sequence |
<@jvlitebutton appjar="${content.jvl}" params={ "permissions":"all-permissions" , "file":"RF00031_folded.stk" , "defaultColour":"Purine/Pyrimidine" , "showAnnotation":"true" , "windowHeight":"515" , "windowWidth":"650" , "showConservation":"false" , "showQuality":"false" , "showConsensus":"true" , "showFullId":"false"} prots=false /> | Displays an RFAM RNA fold family with secondary structure annotation |