Move HMMER release notes into HMMER/; add BATH 1.0 and 2.0 notes

release-notes/RELEASE-1.0.md

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+# BATH 1.0 release notes (Feb 2025)
+
+BATH 1.0 is the first release of BATH. It is essentially a fork of the
+HMMER 3.4 code base, extended to perform translated search (protein
+query against DNA target) directly. bathsearch takes a protein query
+and a DNA target and reports hits in the coordinates of the target
+DNA. There is no need to compute ORFs in all six translation frames
+first, and no bookkeeping to map hits on those ORFs back to the
+encoding genome.
+
+BATH also introduces novel frameshift-aware algorithms to detect
+frameshift-inducing nucleotide insertions and deletions (indels).
+
+Programs in this release: bathbuild, bathconvert, bathfetch, bathstat,
+and bathsearch.

release-notes/RELEASE-2.0.md

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+# BATH 2.0 release notes (May 2026)
+
+This directory holds BATH release notes. The notes for HMMER, from
+which BATH is derived, are in the HMMER/ subdirectory.
+
+
+## new features:
+
+* Spliced alignment. With the new `--splice` option, bathsearch
+  models intron splice sites (GT-AG, GC-AG, and AT-AC, with empirical
+  signal probabilities) and joins ORF hits across introns into
+  gene-level exon chains. The new `--exontblout <f>` option writes a
+  tabular file with one row per exon, and `--min_intron <n>` and
+  `--max_intron <n>` bound the intron lengths considered. A single
+  search cannot yet combine `--splice` and `--fs`.
+
+* SIMD acceleration of the frameshift-aware and spliced dynamic
+  programming kernels: AVX, AVX2, and AVX-512 implementations on x86,
+  and NEON on ARM, with automatic fallback to SSE where newer
+  intrinsics are unavailable.
+
+* A local bias filtering stage that recomputes composition bias over
+  just the aligned region, to better reject short repetitive false
+  positives.
+
+* A new Forward-stage filter (F4): at least one ORF in a window must
+  pass a standard Forward P-value threshold before bathsearch
+  promotes the window to the frameshift or spliced Forward stage.
+
+* Reworked ORF and DNA window construction, including handling of
+  degenerate nucleotides: ORFs no longer span long runs of degenerate
+  nucleotides, and split codons in spliced alignments may contain
+  them.
+
+
+## changes:
+
+* Frameshift-aware alignment is now opt-in. By default bathsearch
+  performs translated (non-frameshifted) search; `--fs` enables the
+  frameshift-aware pipeline. The frameshift probability is now a fixed
+  internal constant set at model build/convert time, and is no longer
+  a tunable option.
+
+* BATH 2.0 does not read model files built by BATH 1.x; run
+  bathconvert to update them. bathsearch prints this instruction when
+  it reads an old file.
+
+* Removed: PowerPC VMX/AltiVec support; MPI support in bathbuild; the
+  bathsearch bias-filter tuning options `--B1`, `--B2`, `--B3`; and
+  the envelope-coordinate columns in search output.
+
+
+## bug fixes:
+
+* Fixed a bug in local bias filtering.
+
+* Reduced memory use by reusing dynamic programming matrices (the
+  Backward matrix for posterior probabilities, and the Forward matrix
+  for Viterbi alignment when posterior decoding fails).
+
+
+For more information, see the
+[git log](https://github.com/TravisWheelerLab/BATH/commits/main).