Isabell Hummel The error message you've encountered in PopART, which reads "Error parsing sequence data; Tree labels do not match alignment labels," indicates a mismatch between the labels in the tree block and the labels in the alignment block within your NEXUS file. Despite your efforts to verify the labels, it's important to consider additional factors that might be contributing to this error:

1. Case Sensitivity: Confirm that the labels in both the tree block and alignment block match in terms of capitalization. NEXUS format is case-sensitive, so even minor differences in capitalization can cause this error.

2. Label Consistency: Double-check for any labels in the tree block that may be missing in the alignment block or vice versa. Even a single missing or additional label can lead to this error.

3. Whitespace Characters: While you mentioned verifying tabs and spaces, it's advisable to also inspect for any non-visible whitespace characters, particularly at the end of lines or within the labels, as these can sometimes be the source of the issue.

4. Special Characters: Ensure that the labels do not contain any special characters or symbols that might not be recognized correctly by the software.

5. Tree Format: Validate that the tree block adheres to the correct formatting specified by the NEXUS format standards. Ensure that it starts with "TREE" and that the labels are enclosed correctly.

6. Label Length: Some software may impose limits on label length. Examine your labels to ensure they are not excessively long, which could exceed character limits in PopART.

If you've meticulously reviewed these aspects and the error persists, consider recreating the tree block or alignment block from scratch. Occasionally, unnoticed errors can slip into the file during editing. Additionally, verify that you are using the most up-to-date version of PopART, as software updates may address compatibility issues.