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I don't know about the BLAST server you're referring to unfortunately. But another BLAST server, SequenceServer looks quite nice too. And has a bunch of helpful visualisations that you can download directly in png or svg. Source code and installation instructions for this one are at http://sequenceserver.com My opinion is biased because my lab makes ...


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This new tool, CIAlign, talks about some automated removal of gaps in multiple sequence alignments https://twitter.com/thekatybrown1/status/1306215132670889984 https://github.com/KatyBrown/CIAlign


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In A2M format, upper case letters represent matches, lower case letters represent inserts, dashes represent deletions, and dots (or spaces outside the identifier lines) represent gaps aligned to inserts. So, both "-" and "." are essentially gaps, but assumed to have different origin. This information is supplementary, and most MSA ...


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If you want an ungapped alignment, you could do an ungapped alignment (the older read aligners were ungapped, e.g. bowtie). However, I suggest that you don't want an ungapped alignment, you just want a stricter one, here's a few options... Remove/trim poorly aligning sequences. You could try GUIDANCE, which has an explicit model or GBLOCKS for a more simple ...


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You may also find useful the BMGE tool (stands for Block Mapping and Gathering with Entropy). BMGE selects regions in a multiple sequence alignment that are suitable for phylogenetic inference by computing their entropy-like score. This allows to distinguish among biologically expected and unexpected variability for each aligned character. BMGE also ...


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Gblocks is a tool for removing gaps/poorly conserved positions from alignments. Available here. Here is a webserver that runs it for you. It's a bit old, possibly there are others at this point.


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