TEagle 3.8.0

TEagle 3.8.0

Release date: 9 August 2026
Platform: Windows 10/11, 64-bit
License: GNU Affero General Public License v3.0 or later (AGPL-3.0-or-later)
Benchmark evidence: https://doi.org/10.5281/zenodo.21848814

TEagle 3.8.0 provides an evidence-traceable integrated workflow for examining one transposable-element sequence, assessing structural and domain evidence, planning a PCR assay, screening predicted products and recording the inputs, versions, thresholds and checksums behind the result. The component algorithms are established methods. The contribution lies in their integration, explicit evidence contracts, reasoned withholding, sealed provenance and native Windows interface; this release does not claim a new general-purpose classifier.

Release status

Version 3.8.0 supersedes version 3.7.0, which was retracted on 7 August 2026. One bundled development accession had entered the corpus described as held out, and two thresholds that affected calls were absent from the provenance manifest. The v3.7.0 benchmark figures and release assets should not be used. Version 3.8.0 removes the development accession from that corpus and seals the two omitted thresholds.

Every analysis-manifest hash changes in v3.8.0 because the sealed parameter set grew by two. Release review also corrected a LINE corroboration guard: a raw endonuclease hit no longer supports a LINE call unless it is N-terminal to reverse transcriptase on the same strand. Primer rules did not change between v3.7.0 and v3.8.0.

Changes in v3.8.0

• The optional WSL2 backend now requests exact releases of RepeatMasker, minimap2, isPcr, NCBI Datasets, faToTwoBit and ViennaRNA. Status and integrity checks reject version drift, and the micromamba bootstrap verifies its versioned archive before extraction.
• Backend cleanup now removes only TEagle-owned environments, caches, logs, staging files and locks. It preserves the shared micromamba executable and environments belonging to other applications.
• Rebuilding the Windows bundle now handles read-only metadata generated by an earlier PyInstaller build without changing files outside the generated bundle.
• Result-table context menus distinguish copying the selected cell from copying the complete row and use the same machine value written to exports.
• Saved or test primer queues remain readable when optional display metadata is absent; the interface states that the value is missing.
• The provenance manifest now records the standalone terminal-inverted-repeat length threshold and the terminal-repeat seed-search window. An automated coverage check now fails if an applied numeric threshold is absent from the manifest.
• The LINE guard now accepts endonuclease as ORF2p corroboration only when its position and strand form the expected N-terminal EN–RT arrangement; downstream and opposite-strand hits no longer license a LINE call.
• The held-out validation corpus excludes all five bundled development examples. It now contains 43 records carrying 36 distinct literal organism annotations.

The changes introduced in v3.7.0 and retained here include stricter treatment of an uncorroborated reverse-transcriptase hit, corrected benchmark accounting, explicit scoring of abstention, 3′-anchored matching of primers with non-templated 5′ tails, complete sealing of in-silico PCR defaults, retrospective reconstruction of published assays and a paired comparison with TEsorter 1.5.1. The changelog gives the complete change history and separates current v3.8.0 evidence from superseded historical results.

Interpretation and limitations

• The benchmark corpora are curated and non-random. Their results describe the included cases and do not estimate population-level accuracy for arbitrary transposable elements.
• Accuracy among answered cases excludes abstentions. Answered-case accuracy must therefore be read with the corresponding abstention denominator and case count.
• In the paired comparison corpus, neither TEagle nor TEsorter made an incorrect order call. TEagle withheld some calls that TEsorter answered correctly, so this corpus measures a cost of withholding but cannot show that withholding prevents errors.
• Retrospective replay of published primer pairs assesses the plausibility of in-silico product prediction for established assays. It does not provide prospective wet-lab validation of primers designed by TEagle and does not establish de novo primer-design success.
• The evidence-traceable classification and assay workflow analyses one locus at a time. The optional landscape module applies a repeat library to a whole genome, but the single-locus benchmark does not validate genome-scale classification performance. TEagle does not perform de novo family discovery, library construction or consensus inference.
• The bundled domain-profile panel is retroviral-tuned. Completeness calls for plant elements may therefore be conservative.
• The installer and executable are not code-signed. Windows SmartScreen may warn on first launch, and managed institutional systems may require approval from local information-technology staff.
• The frozen executable and GUI were exercised on the development Windows host. Clean-machine installation, uninstallation and SmartScreen behaviour were not independently tested for this release.

Distribution

The manually uploaded GitHub release assets are the version-locked Windows installer and the controlled user manual. The release page records the SHA-256 checksum of each asset. The sanitized benchmark evidence is a separate immutable Zenodo record at the DOI above; it is not a software-source archive.

SHA-256 checksums

• TEagle-Setup-3.8.0.exe: A25FDECF27749BF3DDF9D9B2A6C3587F09F8913825BD7B1E999D581FC6D38F39
• TEagle-User-Manual.pdf: 738A96EAEFA44D988872BAC7555013EAE8F8D364AA4457C69CFDAA91959CF746