TEagle v3.6.0

Two development cycles reach release together: 3.5.0 was an internal step and was never tagged, so this release carries both. Provenance manifest hashes change, and results change for elements whose diagnostic structure was not detected. No element loses a call and no superfamily assignment changes.

Classification: four order-level defects, found by benchmarking against an external classifier

A chromodomain now names the LTR order. Chromoviruses are a Ty3/Gypsy lineage and non-LTR elements do not carry the domain, so its presence is informative on its own.

A lone reverse transcriptase is no longer called a LINE. The LINE branch read an absent integrase as evidence of absence rather than as no evidence, which is a different claim.

A terminal inverted repeat can now name a non-autonomous Class II element. Requiring a transposase excluded exactly the elements that do not encode one.

Over the benchmark corpus, order-level accuracy rose from 0.855 to 0.980 and negative-control abstention from 72.7% to 90.9%. Current figures after corpus restratification are 0.986 (0.922-0.997) over 94 gradable cases; benchmarks/raw/scores.json is the authority.

Assay path

A primer carrying a non-templated 5' tail could bind for the first time. The matcher required the whole oligo to match the template, so any pair with a restriction site, adapter or promoter tail predicted no product at all. Binding is now anchored at the 3' end.

In-silico PCR sealed only the parameters the caller typed, so a run left entirely at defaults recorded almost nothing. It now seals the resolved values.

Provenance

The seal recorded twenty of the twenty-one thresholds that decide a call: the upper bound on terminal inverted-repeat length was applied but never written, so a run could not be reconstructed from its own seal. It is now sealed, and a benchmark enumerates every numeric default across the seven detectors the seal draws from and fails if any is unaccounted for.

The stated lower limit of terminal-repeat detection was wrong. The card claimed k-mer seeding stops below roughly 72% identity. That came from a single rough test and is not a constant, because the limit depends on repeat length. Measured over 600 controlled runs on a 574 bp LTR, candidates were still reported at 65% and none at 60%. The card now says so.

Benchmarks

A reproducible suite under benchmarks/ covers the divergence boundary (600 runs), amplicon prediction against 17 published assays from 8 sources, a paired comparison against TEsorter on both database modes, seal stability and coverage, and a sixteen-tool capability matrix in which every cell is sourced. Every figure and table regenerates from raw output with one command; no value is typed by hand.

633 tests across 39 files: 632 pass, one skipped, none fail.

Known issue

The documentation screenshots carry a v3.5.0 header badge rather than 3.6.0. A capture run against this build is still owed.