---
title: "How to Align Peptides"
slug: "how-to-align-peptides"
status: "update"
updated: 2026-10-14T09:22:55Z
published: 2026-10-14T09:22:55Z
canonical: "docs.discngine.com/how-to-align-peptides"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://docs.discngine.com/llms.txt
> Use this file to discover all available pages before exploring further.

# How to Align Peptides

Every peptide SAR Slide is built on an **alignment** — the position-by-position frame that lets Ideation compare peptides of different lengths and compositions. This guide covers the ways to get one — the two computed at import, the two aligners you can run yourself, and importing a file — how to follow an alignment while it runs, how to read the warnings an imported file can raise, how to repair those warnings in the alignment editor, and how to correct which branch a side chain belongs to.

To decide *which* alignment suits your series, see [Understanding Peptide Alignment](/public/docs/explanation-understanding-alignment).

Edit access required

You need **edit access** on the dataset to add an alignment. With view-only access the **New Alignment** button is disabled and reads *"You need edit access on this dataset to add an alignment."*

## Where alignments live

An alignment belongs to the **dataset**, not to a report. One dataset can hold as many alignments as you like, and each SAR Slide picks one of them — so two slides in the same report can use different alignments over the same peptides.

You manage them from the **Alignment** section, which appears in three places:

- the **Alignments** tab of the dataset page, to create, follow, open and delete them outside any report;
- the **Create New SAR Report** dialog, when you are creating a report;
- the **Alignment** tab of the SAR Report settings (**Settings → Alignment**), once a report is open.

All three show the same list of alignments, newest first. Each row carries:

- a **source badge** — **Imported** for a file you uploaded, **Center-star** or **PepSeA** for an alignment Ideation computed (hover the badge for a one-line description);
- the alignment's name, and a status when it is not complete: **In progress**, **Failed** or **Replaced**;
- a summary line: date · *N* peptides · *N* positions (· *x*/*y* branches aligned, for datasets with branches), followed on a PepSeA row by a settings icon you can hover to see the strategy and gap penalty it ran with.

The icons on the right open the alignment editor (**Edit alignment**, on a completed alignment), show the progress or the failure of a computed one, take a replaced request to the alignment that replaced it, and remove the alignment (**Delete alignment**).

![The Create New SAR Report dialog with a peptide dataset selected, showing the Reference Peptide selector and the Alignment section with its list of alignments](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/create-sar-report-peptide.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

## Option 1: Use the alignments created at import

**Every peptide dataset arrives with two alignments queued for it**: a **Center-star alignment** and a **PepSeA alignment**. They are computed in the background once the dataset is ready, so the dataset opens straight away and the two rows show **In progress** until they complete. The center-star one usually finishes first; the PepSeA one can take longer, as it may wait for the monomer similarity matrix to be rebuilt for the monomers the import brought.

When you create a SAR Report, the newest completed alignment is preselected, so you can generate a SAR Slide without providing any file.

Both are best-effort: an alignment that cannot run ends as a **Failed** row with its reason, and the import still succeeds. Center-star does not run on datasets above 5,000 peptides or with no HELM sequence; PepSeA does not run on datasets with more than 208 distinct non-natural monomers (the default limit). If neither completes, use one of the options below.

## Option 2: Align with center-star

Click **New Alignment** and choose **Align with center-star** (*"Alignment computed from the dataset's own sequences with the center-star algorithm."*).

![The New Alignment button expanded, showing its three menu entries: Import from a file, Align with center-star, and Align with PepSeA](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/new-alignment-menu.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

An **Alignment queued** message confirms the request, a new **Center-star alignment** row appears in the list, and its progress opens. Center-star asks nothing: it derives its gap costs from the dataset itself.

Use this when the dataset was imported before automatic alignment existed, when the import-time alignment failed, or when you want a fresh computed frame to compare against a curated one. For how it works, see [Understanding Center-Star Alignment](/public/docs/explanation-understanding-center-star-alignment).

## Option 3: Align with PepSeA

Click **New Alignment** and choose **Align with PepSeA** (*"Alignment computed by MAFFT through PepSeA, using the tenant similarity matrix."*). If the entry is greyed out, its caption says why — the dataset uses more distinct non-natural monomers than PepSeA supports.

The alignment is queued at once, and the **PepSeA alignment parameters** dialog opens. The similarity matrix is already being prepared while you choose, so taking your time here does not delay the result.

![The PepSeA alignment parameters dialog, with the Alignment strategy buttons Accurate, Fast and Automatic, the Gap penalty slider marked Loose, Compact and Very compact, and the Cancel and Start Alignment buttons](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/pepsea-parameters-dialog.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

1. Under **Alignment strategy**, keep **Accurate** for a normal SAR series, or pick **Automatic** or **Fast** for a large dataset. Above 200 peptides, Accurate shows a warning recommending another strategy; you can still run it.
2. Under **Gap penalty**, keep the default **Compact**, move to **Very compact** for a tighter frame, or down to **Loose** for a looser one.
3. Click **Start Alignment**. A **PepSeA alignment started** message confirms it, and the alignment's progress opens.

**Cancel** discards the queued alignment. The **What do these do?** link in the dialog opens [Understanding PepSeA Alignment](/public/docs/explanation-understanding-pepsea-alignment), which explains each setting and which strategy suits which dataset.

The fields depend on your organisation

Your administrator decides which settings the dialog shows, their defaults and which strategies are offered, so your dialog may differ from the one above. If the dialog shows an error instead of fields, your organisation's PepSeA settings could not be read: cancel, and ask your administrator to check the `PEPTIDE_ALIGNMENT_PARAMS` setting.

Running PepSeA again while a previous PepSeA request on the same dataset is still queued replaces that request: its row is marked **Replaced** and links to the new one.

## Follow an alignment in progress

A computed alignment runs in the background, so you can keep working while it does. Its row reads **In progress**; click the progress icon on the row to open the steps it goes through:

| Aligner | Steps |
| --- | --- |
| Center-star | **Queued → Aligning** |
| PepSeA | **Queued → Refreshing distance matrix → Aligning → Aligning branches** |

**Aligning branches** counts the branch groups as it goes, and is left out for datasets without branches. A PepSeA alignment waiting for the similarity matrix shows **Queued** until the matrix is ready.

The progress closes on its own when the alignment completes, and the row's **Edit alignment** icon appears. If it fails, the row reads **Failed**: click its red icon to read why, delete the row, and run a new alignment. The most common reasons are explained in [Understanding PepSeA Alignment](/public/docs/explanation-understanding-pepsea-alignment) and [Understanding Center-Star Alignment](/public/docs/explanation-understanding-center-star-alignment).

Computing never overwrites

Computing an alignment always **adds** one — it never overwrites or replaces a completed alignment, and imported alignments are left untouched. Repeated runs produce same-named rows; remove the ones you don't want with the row's delete icon.

## Option 4: Import an alignment from a file

Click **New Alignment** and choose **Import from a file** (*"Use an alignment you already have, as CSV or Excel"*).

### File format

The layout is the same for CSV and for each Excel sheet:

- **Column 1** holds the structure's **primary identifier** — the ID Ideation matched your peptides on at import.
- **Every following column is one alignment position.** The header labels the position; they must all be non-empty and unique.
- **Each cell holds one monomer symbol.** A hyphen (`-`) is a gap; an empty cell is read as a gap too.
- A file needs at least 2 columns (the ID plus one position).

```
ID,1,2,3,4,5
PEP-001,A,G,V,-,L
PEP-002,-,G,V,A,L
```

Use the **Download template: CSV | Excel** links in the dialog to start from a valid file. The Excel template ships with two sheets, `backbone` and `branch_1`, to show the multi-sheet layout.

| Format | What it covers |
| --- | --- |
| **CSV** (`.csv`) | Backbone only. |
| **Excel** (`.xlsx`) | Backbone **and** branches — one sheet per chain. |

Uncompressed files only

The alignment file must be an **uncompressed** `.csv` or an `.xlsx`. A gzipped `.csv.gz` is rejected with *"Unsupported file format: .gz. Use .csv or .xlsx."*

### Step 1: Choose the file and name it

Pick the file and fill in **Alignment Name** — it is pre-filled from the filename, and it is the name you will see in the Available Alignments list, so make it meaningful.

![The Import Alignment dialog with a selected CSV file, the CSV and Excel template links, the CSV-versus-Excel guidance note, and the Alignment Name field](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/import-alignment-dialog.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

A CSV, or an Excel file with a single readable sheet, imports from here in one click. A multi-sheet Excel workbook walks two more steps first.

### Step 2 (Excel): Choose the backbone sheet

Ideation cannot guess which sheet is the backbone, so it asks: **"Which sheet holds the backbone alignment?"** Each candidate is listed with its shape, so you can recognise it by size.

![The backbone sheet step of the Import Alignment wizard, listing each sheet with its row and position counts plus the No backbone sheet option](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/import-alignment-backbone-sheet.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

Choosing **No backbone sheet, align it to left** tells Ideation to rebuild the backbone frame from the dataset's own HELM sequences and treat every sheet in the file as a branch sheet.

Sheets that could not be read at all are listed under **Ignored sheets:** with the reason.

### Step 3 (Excel): Map the branch sheets

Ideation detects the dataset's real branches on the chosen backbone frame and asks you to say which sheet aligns each one. Every branch gets a dropdown listing the remaining sheets plus **Align at left**.

![The branch mapping step, with one row per detected branch, a sheet dropdown for each, and a warning about a sheet mapped to no branch](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/import-alignment-branch-sheets.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

A sheet can align at most one branch, so assigning it to a branch releases it from any other. Sheets you leave unassigned are called out explicitly — *"Sheet "branch_2" is not mapped to any branch and will not be imported."* — rather than being dropped silently.

Click **Import Alignment** to finish.

## Review the import warnings

**Importing is non-blocking.** A file that does not perfectly agree with the dataset is still imported: the peptides that match are stored, and every discrepancy is recorded as a warning on the alignment. Only genuinely unusable input fails — a file that cannot be parsed, or one where *no* identifier matches any structure in the dataset.

So the import ends one of two ways:

- **Alignment imported successfully** — nothing to review.
- **Alignment imported with warnings — review them in the alignment list** — the alignment is there, and its row now carries an amber warning icon.

![The Available Alignments list with an imported alignment carrying an amber warning icon, alongside the Center-star and PepSeA alignments created at import, and the imported-with-warnings notification](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/alignment-list-warnings.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

Click the amber icon (**View import warnings**) on the row to reopen the **Import Warnings** dialog at any time — the warnings are stored with the alignment, not just shown once.

![The Import Warnings dialog listing three warnings: structures absent from the alignment file, unknown identifiers in the file, and a sequence mismatch](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/import-warnings-dialog.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

| Warning | What it means | What to do |
| --- | --- | --- |
| **Structures absent from the alignment file** | Dataset peptides your file didn't mention. They were added **unaligned**, with their monomers laid out from position 1. | Add them to the file and re-import, or align them by hand in the editor. |
| **Unknown identifiers in the file** | Rows whose ID matches no structure in the dataset. They were ignored. | Usually a typo or a row from another dataset — check the IDs. |
| **Sequence mismatch** | The monomers a peptide has in the alignment differ from the monomers it actually has in the dataset. The warning lists how many monomers and peptides each kind affects: replacements, additions and deletions. | **Fix it in the alignment editor**, all kinds at once or one kind at a time — see below. |
| **Excluded: no monomer sequence** | Dataset peptides with no usable HELM sequence. They were left out of the alignment entirely. | Nothing to do here — fix the peptide's HELM at the source if it should be analyzed (see [HELM Rules for Peptide Import](/public/docs/reference-helm-rules)). |
| **Ignored sheet** | An Excel sheet was skipped, with the reason; or a sheet was mapped to no branch. | Re-import with the sheet mapped, if it should have been. |
| **Backbone not common** | Some peptides don't share the dataset's common backbone, so their branch columns may be misaligned. | Review those peptides; consider importing an explicit backbone sheet. |

Only the first 10 identifiers are listed in each message, followed by *"(and N more)"*.

PepSeA alignments can carry warnings too

A PepSeA alignment shows the same amber icon when PepSeA could not place some rows: peptides or side chains it returned too short are kept, but shown with their full sequence from the first position, so their columns do not line up with the others; and side chains that could not be placed on the aligned backbone are left out. Re-running PepSeA does not change these. Align those peptides by hand in the editor, or use another alignment.

## Fix a sequence mismatch in the alignment editor

A **sequence mismatch** is the one warning you repair directly in Ideation, and the alignment editor is built for it. Open it with the pencil icon (**Edit alignment**) on the alignment's row.

![The alignment editor showing the per-position grid with rows flagged by warning icons and mismatching cells bordered by kind, and the side panel with its Sequence mismatches, Configuration and Filters sections](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/alignment-editor.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

The table takes the left of the editor. A side panel on the right holds three collapsible sections: **Sequence mismatches** (shown only while some peptides matching the **Filters** differ from their dataset sequence), **Configuration** and **Filters**. The sliders icon at the right end of the toolbar hides or shows the panel, and dragging its left edge makes it wider or narrower.

The editor makes each disagreement visible:

- Affected **rows** carry an amber warning icon (*"This alignment differs from the dataset sequence"*).
- The offending **cells** have a coloured border, one colour per kind of mismatch: orange for a replacement, blue for an addition, and red for a deletion (on the cell the missing monomer belongs before). A cell that is both a replacement and the cell before a missing monomer shows the replacement colour, and a monomer missing from the end of a sequence has no bordered cell. The per-kind **Fix** buttons use the same colours, so they also serve as the legend.
- The **Sequence mismatches** section, at the top of the side panel on the right, has a **Show** list to display only the peptides with warnings, or only those with replacements, additions or deletions. The kind options and **Only the N peptides with warnings** show their peptide count; **All peptides** has none. A kind with no peptides left is greyed out. If the kind you selected runs out of peptides, for example after you fixed them, the table shows all peptides again; an undo that brings the kind back restores your choice.
- Its **Highlight mismatches** switch removes the amino acid colours from the table, so the coloured borders are the only colour left.

### Repair everything at once

In the **Sequence mismatches** section, click the **Fix All** button, which reads the count, for example **Fix All 3 peptides with warnings** (or **Fix All 1 peptide with a warning**). Ideation applies every repair needed to make the shown rows match their dataset sequences: wrong monomers are replaced, surplus ones removed, and absent ones inserted. It reports what it did — *"Fixed N rows. Save alignment to persist."* — and the repairs are yours to review before you commit them.

### Repair only some kinds of mismatch

Each difference between the alignment and the dataset sequence is one of three kinds, named from the alignment's side:

| Kind | In the alignment | Repair |
| --- | --- | --- |
| **Replacement** | A different monomer than in the dataset | Replaced with the dataset one |
| **Addition** | An extra monomer, not in the dataset | Deleted |
| **Deletion** | A dataset monomer is missing | Inserted back |

Below **Fix All**, one button per kind (**Fix Replacements**, **Fix Additions**, **Fix Deletions**) repairs only that kind, and shows how many shown peptides need it. Hover a button to see what the kind means.

The kinds follow how the alignment lines up with the dataset sequence: a run of different monomers of the same length counts as replacements, not as additions and deletions. After a partial fix, the remaining differences are counted again, so their kinds can change.

Fix All follows the filter

**Fix All** and the per-kind buttons only touch the rows currently **on display**. Filter the table first if you want to repair a subset, and the buttons' counts follow your filter.

### Edited rows stay on screen

Editing a peptide never hides it, even when the edit makes it stop matching the **Show** list or the **Filters**: the row stays, faded, so you can check the result of your edit. An icon next to its name says what it no longer matches: a crossed-out filter for the **Filters**, a crossed-out eye for the **Show** list.

![Two edited rows kept on screen, faded: one marked with a crossed-out filter icon as it no longer matches the position filter, one with a crossed-out eye as it no longer has the additions the Show list selects, and the Re-apply filters button enabled in the Filters section](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/alignment-editor-faded-rows.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

Fixes, gaps and undo all work on faded rows, and an undo or a later edit that makes the row match again brings back its colours. The bulk actions still act on every row on display, faded ones included.

A position filter stays on its position number: adding or removing gaps moves the monomers, not the filters. An edit that removes a filtered position altogether, for example by removing the gaps of the last position, removes its filter too, and the table is filtered again.

The table is filtered again only when you change a filter or the **Show** list, switch to another chain (the backbone or a branch), or click **Re-apply filters** at the top of the **Filters** section. Re-applying hides the faded rows and shows the peptides that match now. The button is enabled while re-applying would change the table for the **Filters**: a row is faded for the **Filters**, or a hidden peptide matches again, which an undo or redo can do. A row faded for the **Show** list alone does not enable it; it goes the next time the table is filtered again, for example when you change the **Show** list.

### Repair one cell at a time

Click (or right-click) any cell to open its menu. Repair entries appear only when they apply to that cell:

![A cell menu open on a mismatching cell, offering to replace the monomer with the one from the dataset sequence, add a gap, or filter on the value](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/alignment-editor-cell-menu.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A04%3A00Z&se=2026-10-27T13%3A04%3A00Z&sr=c&sp=r&sig=upW3X7BFgj0rg8Kxu%2B4BVvmScZShdu%2F%2FQlLMKJAj%2ByI%3D)

| Menu entry | When it appears |
| --- | --- |
| **Replace with "X" from the dataset sequence** | The cell holds the wrong monomer. |
| **Delete this monomer** | The monomer isn't in the peptide's dataset sequence at all. |
| **Add "X" monomer before** | A dataset monomer is absent from the alignment at this point. |
| **Add "X" monomer at the end** | A dataset monomer belongs past the last position. |
| **Add gap before this position** / **Remove gap** | Always / on a gap cell — for shifting monomers without changing them. The new gap goes before the clicked cell, which moves one position to the right with everything after it. |
| **Filter on "X" at pos N** | Always — narrows the table to peptides carrying that monomer there. |

### Read the branch markers

Two red markers tell you where a side chain joins the backbone, one on each side of the bond:

| Marker | Where | Means |
| --- | --- | --- |
| **B1**, **B2**, … in the top-right corner | On the **backbone** row, on the residue the branch hangs off | *"Branch 1 attached here"* — this residue carries the branch. |
| ***** in a top corner | On a **branch** row, on the residue that carries the bond | *"Branch 1 attaches to the backbone here"* — this is the branch's own bond. |

The asterisk's corner tells you which end of the chain is bonded: **top-left** when the branch joins through its first residue, **top-right** when it joins through its last. Leading gaps do not count — a branch padded with a gap still marks its first real residue on the left. Both markers, and the bridge and chemical-object indicators alongside them, follow your gap edits as you make them.

### Correct which branch a side chain belongs to

Ideation groups side chains into branches by where they attach and what they look like, and that grouping is a guess: two peptides whose side chains you consider the same series can land in different branches, and one branch can hold chains you would rather separate. You correct that here rather than by re-importing.

Click (or right-click) the **backbone cell a branch hangs off** — the cell marked with the branch badge — and the menu offers **Reassign branch**. (When a cell carries more than one branch, each gets its own entry, named after it: **Reassign Branch 2**.) Expanding it lists where the side chain can go:

| Target | What it does |
| --- | --- |
| **Move to Branch N** | Puts this peptide's side chain in that branch, so it aligns with its members. |
| **New branch** | Splits this side chain off into a branch of its own. |

Only moves that change something are listed, so the action never appears to do nothing: a branch the peptide already carries is not offered (its side chain is already there), and **New branch** appears only when the branch being left has other members — moving its last member would simply rename the branch. A branch with no move left to offer shows no entry at all.

The change is local until you save, like every other edit in the editor.

Right-clicking a **position header** instead gives you column-wide actions: **Add gap before this position for all peptides** (the clicked column and everything after it move one position to the right), **Remove this position gaps for all peptides** (for currently displayed peptides when a filter is active), sorting, **Remove filter**, and **Set as first position**.

### Customize position numbering

The **Position numbering** settings, in the **Configuration** section of the side panel, let you:

- **Set the first position**: Choose which column displays as position 1 (or 0); you can also right-click a position header and pick **Set as first position**. It is only available for the backbone: a branch is always numbered from its own first monomer, and on a branch tab the setting reads *Only available for backbone*.
- **Start numbering at 0**: Toggle this option to show positions as 0, 1, 2, … instead of 1, 2, 3, … It applies to the backbone and to the branches (B0, B1, …), in the editor, the peptide viewer, the peptide list and the filters.

**Start numbering at 0** has a default that depends on where the alignment comes from:

- A **new automatic** alignment starts at 0. Alignments created before this release keep numbering from 1 until you change the setting.
- An **imported file** starts at 0 only when its first position column is headed exactly `0`, and at 1 otherwise. A file whose positions run from a negative number (for example -2, -1, 0, 1) is read as starting at 1; this is a known limitation.

These settings apply when you save the alignment, so both you and your teammates see the same numbering next time you open it.

Every change is local until you save, and the outlines disappear as soon as a cell agrees with the dataset. Use **Undo (Ctrl+Z)**, **Redo (Ctrl+Y)** and **Revert all changes** freely.

### Save

- **Save alignment** overwrites the alignment you opened. An alignment belongs to the dataset, so this changes every SAR Report that uses it, not only yours: Ideation asks you to confirm first, and **Ctrl+S** opens the same confirmation as the button.
- **Save as new** keeps the original and stores your edits under a new name (pre-filled as *"«name» - copy"*).

When you save, Ideation re-checks the sequences and **drops the sequence-mismatch warning once every peptide agrees** — that is how the amber icon clears. The other warnings describe the file you imported rather than the sequences, so they stay on the alignment. Re-checking also happens on **Save as new**, so copying an alignment cannot be used to shed a warning it still deserves.

Mismatches can be saved

You can save an alignment with mismatches still in it. Nothing forces you to repair them — the warning simply stays visible so the next person knows.

## Next steps

- [Understanding Peptide Alignment](/public/docs/explanation-understanding-alignment) — the three sources compared, and which one to use
- [Understanding Center-Star Alignment](/public/docs/explanation-understanding-center-star-alignment) and [Understanding PepSeA Alignment](/public/docs/explanation-understanding-pepsea-alignment) — the methods behind the computed alignments
- [How to Create a Peptide SAR Report](/public/docs/how-to-create-peptide-sar-report)
- [How to Explore the Peptide Viewer](/public/docs/how-to-explore-peptide-viewer)
- [Understanding Peptides in Ideation](/public/docs/explanation-understanding-peptides)