The Align package contains utilities for sequence alignment. For instance, if you want to find a piece of sequence in a matrix in Mesquite within a chromatogram viewer of Sequencher, do the following: select the sequence in Mesquite, choose Copy Sequence, then go to Sequencher, select Find Bases, and paste the sequence as the search string. This style of copying is useful when interacting with programs like Sequencher (TM). That is, whereas the standard Copy would place into the clipboard selected pieces of the matrix in tab-delimited text format (e.g., if the sequence AATCA is selected, "A-tab-A-tab-T-tab-C-tab-A" would be copied), this modified Copy Sequence command does not include tabs (thus, "AATCA" would be copied). The Display submenu of the Matrix menu contains other options such as a Bird's eye view which makes the cells narrow to show more of the sequences.Ĭopy Sequence (at bottom of Edit menu) copies the selected cells of the matrix into the computer's clipboard as a sequence. Cells can be colored according to the state at the site ( Color Cells submenu, Character State) or according to a value like the GC bias (Color Cells submenu, Cell Value can request this coloring to use a moving window). The view of the matrix can be adjusted in various ways. You can also apply the other editing tools described for character matrices. Other options may appear see the page on characters for standard choices in this submenu.
CHROMATOGRAM VIEWER IN SEQUENCHER NOT AVAILABLE MANUAL
Shift Other to Match - Shifts other sequences to match a region in a selected sequences described in the manual for the Align package.Remove Gaps-Only Characters - Removes from the matrix all characters that consist of nothing but gaps.Collapse Gaps - collapses gaps in the selected block by pushing all sites to the left, to to yield unaligned sequences.Reverse Complement (DNA matrix only) - reverses the order of contiguously selected blocks of sequence and complements the sequence.These are available under the Alter/Transform submenu of the Matrix menu (some of these may be under "Other Choices"): The following can be applied to all or the selected portions of a molecular sequence matrix in the Character Matrix Editor. The Character Matrix Editor can be used to edit a molecular sequence matrix. It can also be exported to some of these formats. Molecular data can be imported from files of NBRF, FASTA, GenBank/GenPept, PHYLIP, CLUSTAL, and simple table format. Other tools for managing molecular matrices.Combining molecular matrices and sequences.Most of the features discussed elsewhere concerning editing and analysis of general categorical data also apply to molecular data here we focus on features specifically designed for sequence data. Molecular data (DNA or protein sequences) can be edited, manipulated, simulated and analyzed in various ways in Mesquite.