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We've made a short video demonstrating some of the cool things you can do in Geneious (http://www.geneious.com) that as far as we're aware either aren't available or aren't as well implemented in other software. The full 7 minute video is at https://www.youtube.com/watch?v=D5ZB8j4mxBI but a condensed version of the features most relevant to this site (e.g. circular reference sequence mapping, iterative mapping, coverage overview graph, phased SNP variant effects, nice indel visualisation) is at https://www.youtube.com/watch?v=IOGmxjK3f_4
Note that Geneious is commercial software. Some of the features demonstrated (e.g. nice indel visualization, hiding columns over x% gaps, coverage overview graph) are available in the free (unlicensed) version of Geneious. The other features can be used in the fully functional version which has a two week trial in case you feel like trying them out on your own data sets.
Note that Geneious is commercial software. Some of the features demonstrated (e.g. nice indel visualization, hiding columns over x% gaps, coverage overview graph) are available in the free (unlicensed) version of Geneious. The other features can be used in the fully functional version which has a two week trial in case you feel like trying them out on your own data sets.