Resulting alignments, and uploaded alignments in HSAML format, can be displayed and post-processed using a powerful alignment browser. The alignments are shown alongside the guide tree relating the sequences; the tree is interactive and allows control of the information tracks displayed. (A) The site-wise alignment reliability is indicated in shades of grey (bottom). Unreliably aligned sites are deselected (columns marked grey) using an adjustable threshold (drop-down 'Reliability' menu) and the remaining sites can be exported in various alignment formats for downstream evolutionary analyses. (B) Using the FAST/SLOW/CODON model, inferred sequence structure for genomic DNA alignments is indicated in shades of green, red and blue (bottom). A prediction for a pre-computed EPO alignment  shows a correctly inferred change from the FAST state (green) in the intron through the SLOW state (red) at the splice site to the three CODON states (blue) in the exon.
Löytynoja and Goldman BMC Bioinformatics 2010 11:579 doi:10.1186/1471-2105-11-579