Sequence ID Renaming

Desktop

ABCDE

Phone

ABCDE

• ASequences tab
• BTool switcher
• CInput files
• DRun button
• EFile panel

New interface coming soon

This page shows the new SEGUI interface, which is in development. The current release (v1.1.3) looks different, and features marked In development are not available in it yet.

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

Steps

1. Select Sequences in the navigation bar A.
2. Open Rename sequence IDs from the tool list on wide windows, or select the tool name B at the top of the page to switch tools.
3. Add the input files C with Browse files, Browse folder, or Open archive. SEGUI searches a folder and its subfolders for files that match the tool's input format. See file input for mobile options.
4. Select renaming parameters.
5. Select Browse under Select output directory to choose the output folder. On phones and tablets, enter a Directory name instead; SEGUI saves it in the app's own folder.
6. Select the output sequence format.
7. Select the run button D, 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_names	New_names
Genus_species1_random	Genus_species1_voucherID
Genus_species2_random	Genus_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.