2.4.0-alpha.2

SM-2019 update for Galaxy.
Still under active development and not fully ready for use.

2.4.0-alpha.1

Still under active development and not fully ready for use.

2.3.14

Notable Changes

• BGM has been ported to use libv3 library.

Issues Addressed in this Release

• #820 - Problem accessing BGM/Spidermonkey from command line
• #817
• #809

Please see the associated pull request for a complete listing of commits included in this release.

2.3.13

Notable Changes

Please see the associated pull request for a complete listing of commits included in this release.

2.3.12

Notable Changes

• Bug fixes for #789 - Fixes compilation issue on FreeBSD

Please see associated pull request and pull request for a complete listing of commits included in this release.

2.3.11

Notable Changes

• Bug fixes for #743, #746, and #748

Please see the associated pull request for a complete listing of commits included in this release.

2.3.10

Notable Changes

• Bug fix for #738 (Stephen Shank)

Please see the associated pull request for a complete listing of commits included in this release.

2.3.9

Notable Changes

• Bug fixes for #709 and #723 (Sergei Pond and Stephen Shank)

Please see the associated pull request for a complete listing of commits included in this release.

2.3.8

Notable Changes

• LEISR 0.4 (Stephanie Spielman and Sergei Pond)
• Bug fixes for #703 and #712 (Sergei Pond and Steven Weaver)

Please see the associated pull request for a complete listing of commits included in this release.

2.3.7

Notable Changes

• [#696] Five new amino acid models (Stephanie Spielman)

  • "mtMAM" - "Empirical model of protein evolution for mammalian mitochondrial genomes from Yang N, Nielsen R, and Hasegawa M. (1998). Ref: http://dx.doi.org/10.1093/oxfordjournals.molbev.a025888,
  • "cpREV" - "Empirical model of protein evolution for chloroplast genomes from from Adachi et al. (2000). Ref: https://www.ncbi.nlm.nih.gov/pubmed/10795826"
  • "HIVBm" - "Empirical model of protein evolution for between-host HIV sequences from Nickle et al. (2007). Ref: https://doi.org/10.1371/journal.pone.0000503"
  • "HIVWm" - "Empirical model of protein evolution for within-host HIV sequences from Nickle et al. (2007). Ref: https://doi.org/10.1371/journal.pone.0000503"
  • "AB" - "Empirical model of protein evolution for antibody sequences from Mirsky et al. (2015). Ref: https://doi.org/10.1093/molbev/msu340"

• [#683] GARD results formatted to be consistent with other methods (Steven Weaver)

• Bug fixes for #685, #687, #689, and #700 (Sergei Pond)

Please see the associated pull request for a complete listing of commits included in this release.