![]() With a block of the matrix selected, choosing Matrix>Alter/Transform>Collapse Gaps will remove all gaps in the selected block, with the bases or amino acids pushed as far to the left as possible. Removal of Gaps Remove All-Gap CharactersĬhoosing this from Matrix>Alter/Transform>Remove All-Gap Characters will remove all sites in the matrix that consist entirely of gaps. ![]() This feature requires that codon positions be designated. The amount each sequence will be shifted will vary from sequence to sequence. You can also choose Matrix>Alter/Transform>Shift To Minimize Stop Codons to shifts each sequence 0, 1, or 2 bases so as to minimize the number of stop codons. Note that this is not an alignment algorithm it simply shifts the sequences, maintaining whatever gaps are there or not in the sequences to be shifted. For each taxon that it can find such a match, it will shift those sequence such that the matched regions are lined up with the selected region. If you press OK, Mesquite will look at each of the taxa within the range, and see if it can find a portion of each that is at least as similar as the percentage indicated to the selected portion (no gaps allowed). By default the range of taxa is the remaining taxa in the matrix. If you then choose Matrix>Alter/Transform>Shift Other to Match Selected., then you will be presented with a dialog box that lets you choose a range of taxa, as well as a percentage. This tool pushes to the right the entire sequence to the right of the tool, or, if you have the Option key held down, it pushes to the left the entire sequence to the left of the tool. For example, you can also request that the matrix be expanded on either end as necessary as you move sequences around by default this option is off. There are additional options in the popup menu of the tool's button. This tool move move a selected block of cells. You can also request that the matrix be expanded on either end as necessary as you move sequences around by default this option is off. There are additional options in the popup menu of the tool's button that allow you to request that entire sequences are moved, or all sequences on one side. If you hold the Option key down, then all sequences other than those delimited will be moved. This tool allows one to draw a line between two sites, through one or more sequences, as shown in the following image: If you wish, you can move more than a single, contiguous block by turning on "Move Selected Block" within the tool's popup menu, then using the tool to move selected bases and gaps. If you move the tool between two bases it will let you split a block in two, inserting gaps. This tool will move a contiguous block of a single sequence. There are some visualization features in Mesquite that can aid in manual alignment. (Recalculations will be done once you let go of the mouse button, in any event.) If some of these calculations take a while, this can dramatically slow down use of these tools. If this is chosen, then all calculations (e.g., charts, character tracings, etc.) that depend upon these data will be redone as you use these tools. These tools have a "Live update analyses, etc." option in their popup menus. There are several tools available for moving bases by hand. Manual Alignment Tools Moving bases by hand
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