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Sequence ID Renaming

A quick way to rename sequence IDs in across many alignments.

Steps​

  1. Select the Alignment button from the navigation bar.
  2. Select Rename sequence IDs from the dropdown menu.
  3. Add the input files by clicking the Add file button. On desktop platforms, you can also input a directory by clicking the Add directory button. The app will look for matching files in the directory.
  4. Select renaming parameters.
  5. Add the output directory by clicking the Add directory button.
  6. Select the output sequence format.
  7. Click the Run button labeled Rename to start the task.

Renaming Parameters​

Input file​

Example input file:

The first column should be the original IDs and the second column should the new IDs. Save as .tsv or .csv. For example:

Original_namesNew_names
Genus_species1_randomGenus_species1_voucherID
Genus_species2_randomGenus_species2_voucherID
tip

You can use the sequence ID extraction feature to generate all the unique sequence IDs in your dataset. Then, input the file into an Excel sheet and add the new names in the second column.

Remove text​

You can remove a specific text from the sequence IDs. For example, you can remove _contigs from all the sequence IDs.

Remove regular expression​

Use the regular expression to remove a specific pattern from the sequence IDs. For example, you can remove ^locus[0-9] from all the sequence IDs. This will remove all the sequence IDs starting with locus followed by a number. If you select remove all matches, it will remove all the matches found in a sequence ID. Otherwise, it will remove the first match found in a sequence ID, then continue to the next sequence ID.

Find and replace a matching text​

You can find a specific text and replace it with another text. For example, you can replace locus01 with locus.

Find and replace regular expression​

Use the regular expression to find a specific pattern and replace it with a string. For example, you can replace ^locus[0-9] with locus. This will replace all the sequence IDs starting with locus followed by a number with locus. Similar to other regular expression options, you can select replace all matches to replace all the matches found in a sequence ID.