You can save multiple sequence alignments in the MSA editor window in one of the following formats:
- MacVector binary format
- FASTA
- PHYLIP
- NEXUS
- ASCII 1-letter
- Staden
- GCG (MSF)
- GenBank
- EMBL/SWISSPROT
- NBRF .
For all formats except PHYLIP, you save MSA documents in exactly the same way as single sequences. If you set Format to PHYLIP, the Options button in the File | Save As dialog box for MSA documents becomes enabled.
When saving aligned sequences as a PHYLIP file, you need to set the namelength (the length of the field containing the sequence names). If the value you enter is less than the length of any of the current sequence names, they will be truncated. In cases where truncation would result in two or more sequences being given the same name, MacVector will append numbers to the truncated name to distinguish the different sequences. Before saving as a PHYLIP file, you also need to indicate whether the sequences should be interleaved or non-interleaved.
TO SAVE a multiple aligned sequence as a PHYLIP file
1. Ensure the required MSA editor window is active.
2. Choose File | Save As to display the Save As dialog box.
3. If required, navigate to the required folder, or create a New folder.
4. If required, change the file name by typing in the Name text box.
5. Choose PHYLIP from the Format drop-down menu.
6. Select Options.
7. Set the interleaving control:
- If you want the sequences to be interleaved, ensure that the check box is selected.
- If you want the sequences to be non-interleaved, ensure that the check box is not selected.
8. Type the required namelength in the PHYLIP namelength text box.
9. Select OK to apply the settings and return to the Save As dialog box.
10. Select Save to save the file.
When you save an aligned sequence file using the Save As dialog box, MacVector will by default add a filename extension appropriate to the format you select, as follows:
FASTA, FASTP .fa; PHYLIP .phy; NEXUS .nex; ASCII .asc; Staden .sta; GCG (MSF) .msf; GenBank, GenPept .gb; EMBL .emb; SWISSPROT .swi
These file extensions will be particularly useful when files are used with other operating systems which use extensions to identify the file type.