Several commands in the File menu allow you to export alignments, distance matrices and phylogenetic trees, as well as aligned sequences and the consensus sequence. Unless you wish to export all sequences in the project, you must first make a selection.

Command What is exported?
Alignment Report See Export the alignment report.
Active Block Alignment Report
Active Block Alignment Aligned sequences in the active block with gaps included (Mauve alignments only). This option supports exporting to a wide variety of formats, including FASTA, GenBank, MEGA, MegAlign, MSF and Nexus.
Active Block Subsequences A selected range of the aligned sequences in the active block (Mauve alignments only).
Alignment All aligned sequences, including gaps.
Aligned Subsequences A selected region of the aligned sequences, including gaps.
All Data Aligned sequences, distance table and phylogenetic tree information. Supports Nexus formats (.nex, .nxs) only.
Distance Matrix Matrix information from the Distance view Supports comma- or tab-separated formats (.csv or .tab), PHYLIP format (.dist) or Nexus formats (.nex, .nxs).

After selecting a name and format, click Save to launch the Choose Matrix Form dialog:

Use the drop-down menu to choose whether to save the entire (“square”) matrix or only the upper or lower triangle.

Note: If you choose to save in .dist format, the sample names in the saved file will automatically be truncated to 10 characters.
Selected Sequence(s) Selected individual sequence(s), exported as unaligned individual sequences.
Selected Aligned Sequence(s) Selected aligned sequence(s), including gaps.
Selected Active Block Aligned Sequence Aligned sequences in the selected block (Mauve alignments only), including gaps.
Sequences All sequences in the project, exported as unaligned individual sequences. Supports various GenBank and FASTA formats; MegAlign format (.meg); or Nexus formats (.nex, .nxs).

When exporting to most formats, gaps are represented as embedded dashes. When exporting to GenBank, gaps in nucleotide sequences are represented as “n’s” and those in amino acid sequences are represented as “x’s.”
Tree Phylogenetic tree information from the Tree view. See Export a tree to a tree viewer.

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