Figure 2.

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 [16] 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.

L√∂ytynoja and Goldman BMC Bioinformatics 2010 11:579   doi:10.1186/1471-2105-11-579
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