hyphaltip · Nov 2, 2026 · Oct 29, 2026 · Oct 30, 2026 · Oct 30, 2026 · Oct 30, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/CITATION.cff b/CITATION.cff
@@ -8,7 +8,7 @@ authors:
   affiliation: University of California-Riverside
   orcid: "https://orcid.org/0000-0002-7591-0020"
 title: "MATPredict: MAT locus identification in Fungi"
-version: 0.7.0
+version: 0.8.0
 doi: TBD
-date-released: 2026-10-26
+date-released: 2026-10-31
 url: "https://github.com/stajichlab/MATPredict"
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ idiomorph or mating type it is (for example Plus/Minus, MAT1-1/MAT1-2, HD/PR
 alleles). Every reference record traces to a publication or a validated
 deposit, and every call reports the evidence behind it.
 
-Current release: [`v0.7.0`](https://github.com/stajichlab/MATPredict/releases/tag/v0.7.0).
+Current release: [`v0.8.0`](https://github.com/stajichlab/MATPredict/releases/tag/v0.8.0) (detection code, database and the data, calls and counts shown on the site are those of the v0.8.0 run).
 Changes: [CHANGELOG.md](CHANGELOG.md).
 
 ## Contents
@@ -505,28 +505,28 @@ pixi run -e test pytest -q
 ## Validation and known limits
 
 Measured results (details in [analysis/INDEX.md](analysis/INDEX.md)). The BFD and held-out rows are detection (call) rates from
-the v0.7.0 definitive run, not accuracy: no truth set exists for BFD genomes. Subphylum rates count the classes of each subphylum;
+the v0.8.0 definitive run, not accuracy: no truth set exists for BFD genomes. Subphylum rates count the classes of each subphylum;
 the 7 rust genomes skipped for annotation reasons (#165) are counted as not called. The ground-truth, typing and hold-out rows are
-older measurements and were not repeated for v0.7.0. How each campaign was judged is in
+older measurements and were not repeated for v0.8.0. How each campaign was judged is in
 [results/2026-10_cleanrun_preparation/](results/2026-10_cleanrun_preparation/).
 
 | Test | Result |
 |---|---|
 | Zygomycete ground-truth set (23 genomes) | 23/23 loci and idiomorphs |
-| Held-out LCG Mucoromycotina genomes (never used in curation) | 549/621 called (v0.7.0 run) |
-| Held-out Jena Mucoromycotina genomes | 61/64 called (v0.7.0 run) |
+| Held-out LCG Mucoromycotina genomes (never used in curation) | 549/621 called (v0.8.0 run) |
+| Held-out Jena Mucoromycotina genomes | 61/64 called (v0.8.0 run) |
 | Idiomorph typing validation | 0/540 typed wrong |
 | Pezizomycotina hold-out, order radius | 7/7 |
-| Ascomycota, 19,415 BFD genomes (v0.7.0 run) | 17,592 called (90.6%) |
-| Basidiomycota, 3,275 BFD genomes (v0.7.0 run) | 2,977 called (90.9%): Agaricomycotina 92.2%, Ustilaginomycotina 97.7%, Pucciniomycotina 79.5% |
-| Mucoromycotina, 289 BFD genomes (v0.7.0 run) | 258 called (89.3%) |
+| Ascomycota, 19,415 BFD genomes (v0.8.0 run) | 17,607 called (90.7%) |
+| Basidiomycota, 3,275 BFD genomes (v0.8.0 run) | 2,977 called (90.9%): Agaricomycotina 92.2%, Ustilaginomycotina 97.7%, Pucciniomycotina 79.5% |
+| Mucoromycotina, 289 BFD genomes (v0.8.0 run) | 258 called (89.3%) |
 
 Known limits (open items in [analysis/open-questions.md](analysis/open-questions.md)):
 
 - Only three phyla have curated families.
 - A genome far from every reference often fails the evidence bar, so an
   uncalled genome is weak evidence that the genome has no MAT locus. The full
-  Ascomycota run (19,415 genomes, v0.7.0) leaves 1,751 uncalled and 72 not run.
+  Ascomycota run (19,415 genomes, v0.8.0) leaves 1,736 uncalled and 72 not run.
 - Fragmented assemblies can split a locus or lose its flanking genes.
 - In Mucoromycota, *Absidia* flanking genes are often off-scaffold, and the
   gene order of the Lichtheimiaceae is not yet known.
@@ -550,14 +550,14 @@ No paper describes MATPredict yet. Cite the software and the release you used.
 The citation metadata is in [CITATION.cff](CITATION.cff); GitHub shows it under
 "Cite this repository".
 
-> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.7.0.
+> Stajich JE. MATPredict: MAT locus identification in Fungi. Version 0.8.0.
 > https://github.com/stajichlab/MATPredict
 
 ```bibtex
 @software{matpredict,
   author  = {Stajich, Jason E.},
   title   = {MATPredict: MAT locus identification in Fungi},
-  version = {0.7.0},
+  version = {0.8.0},
   url     = {https://github.com/stajichlab/MATPredict},
   year    = {2026}
 }

diff --git a/misc/considered_discarded/MAT_logo.jpg b/misc/considered_discarded/MAT_logo.jpg
diff --git a/misc/considered_discarded/MAT_logo.png b/misc/considered_discarded/MAT_logo.png
diff --git a/misc/considered_discarded/README.md b/misc/considered_discarded/README.md
@@ -2,7 +2,6 @@
 
 The logo in use is `misc/logo.svg` / `misc/logo.png` (a lens finding the mating-type locus; source files and variants in `web/intro/logo/`). Kept here for reference, 2026-10-26:
 
-- `MAT_logo.jpg`, `MAT_logo.png`: an illustrated emblem (two hyphal trees meeting over "MAT A/+" and "MAT α/-"). Not used: the text in the image says "Mating Type Prediction / Mycology", not "MATPredict", and it is too busy for a favicon.
 - `old_logo_pencil_mushrooms_helix.jpg`: the earlier logo (pencil mushrooms on a DNA helix); its tagline said "using deep learning", which the tool is not.
 - `early-drafts/`: first SVG sketches (a locus badge, two fusing hyphae, a helix).
 - `fable-concepts/`: two further concepts, "fit" (two complementary gene arrows) and "cap" (a mushroom whose spots are gene arrows), with `NOTES.md` giving the idea and weaknesses of each concept including the lens that was chosen.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [project]
 name = "MATPredict"
-version = "0.7.0"
+version = "0.8.0"
 description = "Fungal MAT locus annotator/classifier"
 authors = [{name = "Jason Stajich", email = "[email protected]"}]
 requires-python = ">=3.11"

diff --git a/results/2026-10-31_v080_ascomycota/MANIFEST.txt b/results/2026-10-31_v080_ascomycota/MANIFEST.txt
@@ -0,0 +1,9 @@
+v0.8.0 definitive run, ascomycota campaign
+commit: a2933f7af48df14231ee6923f4578bc0f7b65f6b (branch prep-v0.7.1 = main 6959657 + version 0.8.0; src/db/scripts identical to main)
+worktree: /bigdata/stajichlab/jstajich/projects/MATPredict/.claude/worktrees/run-a2933f7
+DETECT_ARGS: --preset v0.8  (v0.7 policies + cross_family_policy on)
+pixi.lock sha256: 675a15123d22857564dbb020592db9075cd60c8bb82f9cbb53a077abb31f4ac9
+compute: throttled, 3 chains x 16 CPUs = 48 CPUs in flight (submit_throttled.py); jobs: results/2026-10-31_v080_submit/jobs.tsv; submitted 2026-10-31
+note: GCA_023522825.1_DampeI2T2 timed out at the 3600 s genome limit in wave_7/small_006 (16 genomes in parallel; rc=124; v0.7.0 took 771 s). Re-run alone with GENOME_TIMEOUT=14400, same worktree and --preset v0.8 (job 31582728, 2746 s; rerun_timeout/); the report was copied into wave_7/small_006/runs/. Call identical to v0.7.0 (MAT1-1 high, JAMFTM010000001.1:954082-971459).
+db content sha256 (database_digest, candidates excluded): 70afa14e884604f06fa359b083a43317d83458f60b1b0c8254be561d7a131676  (184 records)
+determinism: 24 Ascomycota and 24 Basidiomycota genomes (seed 20261102) run twice on this commit with --preset v0.8: 0 changed loci between the runs and against this campaign (results/2026-11-02_determinism on HPCC)
diff --git a/results/2026-10-31_v080_ascomycota/by_class.tsv b/results/2026-10-31_v080_ascomycota/by_class.tsv
@@ -0,0 +1,31 @@
+class	genomes	reports	called	pct_called	routing	wall_median_s	wall_p90_s	wall_max_s	loci	n_label_unsupported	tier_dropped	tier_dropped_noted	margin_fallback	vote_collapse	polished_model_lost	distant_fragment	high_supported	high_tie_break	high_grey	outside_scope_high_supported	outside_scope_high_tie_break	outside_scope_high_grey	defective_loci
+Sordariomycetes	6016	6012	5626	93.6	lineage:5976; not_searched:36	138	212	2746	5752	114	0	0	0	0	0	0	0	0	0	4362	1	1	2202
+Eurotiomycetes	3220	3214	3104	96.6	lineage:3210; not_searched:4	132	202	610	3302	10	0	0	0	0	0	0	0	0	0	2058	0	0	1507
+Pichiomycetes	2967	2966	2822	95.1	lineage:2652; phylum_fallback:220; direct:91; not_searched:3	32	87	228	3274	31	2	2	0	0	2	0	0	0	0	0	0	0	153
+Dothideomycetes	2731	2730	2587	94.8	lineage:2724; not_searched:6	124	206	2836	2705	326	0	0	0	0	0	0	302	11	0	1855	11	7	552
+Saccharomycetes	2646	2598	2209	85.0	lineage:2246; phylum_fallback:337; direct:14; not_searched:1	23	47	137	4428	191	0	0	0	0	0	0	0	0	0	0	0	0	300
+Lecanoromycetes	479	478	413	86.4	lineage:476; not_searched:2	109	173	259	434	9	0	0	0	0	0	0	0	0	0	260	0	0	179
+Leotiomycetes	435	430	399	92.8	lineage:430	140	244	372	414	16	0	0	0	0	0	0	0	0	0	275	1	0	213
+Dipodascomycetes	398	397	157	39.5	phylum_fallback:225; lineage:168; not_searched:4	35	83	143	159	3	0	0	0	0	0	0	0	0	0	0	0	0	10
+Pezizomycetes	172	172	137	79.7	lineage:169; direct:3	59	105	164	137	2	0	0	0	0	0	0	0	0	0	0	0	0	51
+Schizosaccharomycetes	68	67	66	98.5	direct:59; lineage:8	22	29	45	96	0	0	0	0	0	0	0	0	0	0	0	0	0	7
+Orbiliomycetes	67	67	4	6.0	phylum_fallback:67	145	318	417	4	0	0	0	0	0	0	0	0	0	0	1	0	0	0
+Lipomycetes	59	59	3	5.1	phylum_fallback:59	43	154	298	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+NA	52	48	29	60.4	phylum_fallback:38; lineage:10	119	221	308	32	1	0	0	0	0	0	0	0	0	0	16	0	0	6
+Taphrinomycetes	22	22	5	22.7	lineage:22	19	28	39	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Trigonopsidomycetes	16	16	0	0.0	phylum_fallback:16	34	59	61	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Arthoniomycetes	13	13	8	61.5	lineage:11; not_searched:2	91	157	160	8	1	0	0	0	0	0	0	0	0	0	7	0	0	3
+Geoglossomycetes	12	12	6	50.0	lineage:12	108	163	179	6	0	0	0	0	0	0	0	0	0	0	6	0	0	2
+Pneumocystomycetes	11	11	9	81.8	lineage:11	12	21	22	9	2	0	0	0	0	0	0	0	0	0	0	0	0	0
+Lichinomycetes	10	10	7	70.0	lineage:10	151	271	323	8	1	0	0	0	0	0	0	0	0	0	4	0	0	4
+Candelariomycetes	4	4	4	100.0	lineage:4	131	150	150	4	0	0	0	0	0	0	0	0	0	0	1	0	0	2
+Sporopachydermiomycetes	4	4	4	100.0	phylum_fallback:4	33	64	64	4	2	0	0	0	0	0	0	0	0	0	0	0	0	0
+Alloascoideomycetes	3	3	3	100.0	phylum_fallback:3	46	49	49	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Coniocybomycetes	2	2	2	100.0	lineage:2	96	143	143	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Saitoellomycetes	2	2	0	0.0	lineage:2	12	17	17	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Laboulbeniomycetes	1	1	0	0.0	lineage:1	57	57	57	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Neolectomycetes	1	1	0	0.0	lineage:1	60	60	60	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Novakomycetes	1	1	0	0.0	lineage:1	47	47	47	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Sareomycetes	1	1	1	100.0	lineage:1	102	102	102	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Xylobotryomycetes	1	1	1	100.0	lineage:1	95	95	95	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+Xylonomycetes	1	1	1	100.0	lineage:1	213	213	213	1	0	0	0	0	0	0	0	0	0	0	1	0	0	1