Text format (e.g., if the sequence AATCA is selected, "A-tab-A-tab-T-tab-C-tab-A" Into the clipboard selected pieces of the matrix in tab-delimited That is, whereas the standard Copy would place The selected cells of the matrix into the computer's clipboardĪs a sequence. Which makes the cells narrow to show more of the sequences.Ĭopy Sequence (at bottom of Edit menu) copies Menu contains other options such as a Bird's eye view Value can request this coloring to use a moving window).Įxamples of this are shown below. To a value like the GC bias (Color Cells submenu, Cell CellsĬan be colored according to the state at the site ( ColorĬells submenu, Character State) or according
The view of the matrix can be adjusted in various ways. Other options may appear see the page on charactersįor standard choices in this submenu.
Nucleotide complement (DNA matrix only) -Įnters the complementary sequence into the selected cellsĬharacters at edges of matrix that are gaps-only. Thus, a Y will be converted to a C with 50% probability, and to a T with 50%. Arbitrarily Resolve State Ambiguity - Any cell that has partial uncertainty in the state (e.g., "Y", which is C or T) will be resolved into one of its states, chosen randomly. For example, for a nucleotide sequence, a cell that has both C and T will be converted into "C or T", i.e., Y. Convert Polymorphisms to Uncertainties - Converts all polymorphisms in the selection to uncertainty. For example, for a nucleotide sequence, a Y (C or T) will be converted into "C and T". Convert Uncertainties to Polymorphisms - Converts all uncertainties in the selection to polymorphisms. SEQUENCHER EXPORT FASTA AS ONE FILE 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. Reverses the order of contiguously selected blocks of sequence Menu (some of these are available under "Other Choices"): These are available under the Alter/Transform submenu of the Matrix Of a molecular sequence matrix in the Character Matrix Editor. The following can be applied to all or the selected portions It can also be exported to some of theseĬan be used to edit a molecular sequence matrix. Molecular data can be imported from files of NBRF, FASTA, PHYLIP, CLUSTAL, and simple table format. General categorical data also apply to molecular data here weįocus on features specifically designed for sequence data. Most of theįeatures discussed elsewhere concerning editing and analysis of Simulated and analyzed in various ways in Mesquite. 
Molecular data (DNA or protein sequences) can be edited, manipulated,
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