Issues

• HIVTrace not working

  veg/hyphy#2044 · Filter by author ikb6 opened on Nov 4, 2026
  8

• Contrast-FEL reported q-values disagree with BH FDR site selection (HyPhy 2.5.103)

  veg/hyphy#2038 · Filter by author taki-sh opened on Oct 28, 2026
  1

• Fubar incompatibility of results between version

  veg/hyphy#2037 · Filter by author MartinTes opened on Oct 19, 2026
  1

• 2.5.103: aBSREL multiple-hits result varies between runs on linux-64; HYPHYMPI writes progress to non-TTY stderr

  veg/hyphy#2035 · Filter by author mvdbeek opened on Oct 17, 2026
  1

• Alignment trimming and HyPhy

  veg/hyphy#2033 · Filter by author 00-kelvin opened on Oct 7, 2026
  2

• Finding null expectations for selection tests

  veg/hyphy#2032 · Filter by author qitingcai opened on Oct 7, 2026
  9

• contrast FEL aborted immediately (similar to other issues)

  veg/hyphy#2029 · Filter by author katherinermartin opened on Oct 6, 2026
  2

• Interpreting GARD recombination breakpoints vs rate variation

  veg/hyphy#2025 · Filter by author katherine-li07 opened on Oct 3, 2026
  4

• GARD (MPI) hangs at exit when site-to-site rate variation (GDD) is enabled — analysis completes, process never terminates (2.5.98)

  veg/hyphy#2016 · Filter by author stevenweaver opened on Sep 17, 2026
  1

• How do all of the recent BUSTED methods: E, +S+MH, and PH interact with each other

  veg/hyphy#2011 · Filter by author shjenkins94 opened on Aug 5, 2026
  11