MAFFT Changelog

What's new in MAFFT 7.303

Aug 11, 2016
  • Fixed a bug; version 7.302 could not be compiled if multithread was disabled.

New in MAFFT 7.245 (Jul 22, 2015)

  • Fixed a bug in the combination of --addfragments and --reorder. When remote homologs are added, the order of sequences was confusing. In this version, remote homologs are placed at the end of the output.

New in MAFFT 7.244 (Jun 16, 2015)

  • Changed the parameters for E-INS-i. To disable this change, add the --oldgenarpair option.
  • Added a new option, --addlong.

New in MAFFT 7.221 (Apr 16, 2015)

  • Fixed a bug in an experimental option, --addfull. Versions 7.213 - 7.220 had this bug (2014/Dec - 2015/Apr).

New in MAFFT 7.220 (Mar 30, 2015)

  • Fixed a problem when almost identical sequences are subjected to the iterative refinement options.

New in MAFFT 7.216 (Mar 30, 2015)

  • Made small changes in output of mafft-homologs.rb and --scoreout.

New in MAFFT 7.215 (Dec 18, 2014)

  • Fixed a bug in the combination of --adjustdirection and --anysymbol. Due to this bug, unnecessary texts had been added to title lines.

New in MAFFT 7.213 (Dec 18, 2014)

  • Fixed a problem in the --addfragments option, when a sequence to be added is longer than its closest homolog(s) in the reference alignment. Due to this change, the assumed tree became different between --retree 0 and other cases.
  • Slightly changed the handling of internal gaps in --add and --addfragments options.

New in MAFFT 7.212 (Dec 18, 2014)

  • Fixed a bug in the --addfragments option. In the multithread mode, when the sequences to be added include outlier(s) to the reference alignment, a memory error sometimes occurred due to this bug.

New in MAFFT 7.205 (Dec 18, 2014)

  • Fixed a compilation problem that occurred when multithreading is disabled.

New in MAFFT 7.204 (Dec 18, 2014)

  • Fixed a bug in the --merge option. This option did not work in versions 7.182 - 7.187.

New in MAFFT 7.187 (Oct 2, 2014)

  • Fixed a bug in versions 7.182-7.186 in handling null or empty sequences in the multithread mode.

New in MAFFT 7.164 (Aug 2, 2014)

  • In the --auto mode, thresholds to switch strategies (L-INS-i, FFT-NS-2, etc) have been changed. This version tends to select a slower (more accurate) strategy than previous versions.
  • Changed some warnings and error messages to clearer ones.

New in MAFFT 7.158 (Jun 30, 2014)

  • Fixed a problem in the calculation of sequence weights in the --merge option.

New in MAFFT 7.157 (Jun 30, 2014)

  • Fixed a bug in the --addfragments mode. When the sequences in the reference alignment were almost identical to each other, an incorrect result was occasionally returned due to this bug.

New in MAFFT 7.154 (Jun 30, 2014)

  • Fixed a problem in the RNA alignment options (X-INS-i and Q-INS-i) that occurred when compiled by gcc versions 4.8 or 4.9.

New in MAFFT 7.150 (Jun 30, 2014)

  • Fixed a problem "dyld: Library not loaded: /usr/local/lib/libgcc_s.1.dylib", which occasionally occurred on Mac.

New in MAFFT 7.149 (Jun 30, 2014)

  • Fixed a bug in the regional re-alignment calculation. This feature was not compatible with v7.130 due to this bug.
  • Fixed a problem in the --addfull, to add long sequences into an existing alignment.
  • --addfragments in a case where a sequence to be added is longer than its closest homolog(s) in the reference alignment.

New in MAFFT 7.130 (Jun 30, 2014)

  • An experimental option to avoid aligning non-homologous segments, --unalignlevel f (0.0 ≤ f ≤ 1.0; f=0.0 by default). Appropriate value of f is 0.5-0.8?

New in MAFFT 7.123 (Jun 30, 2014)

  • Made a change in --similaritylevel in the nucleotide mode.

New in MAFFT 7.122 (Oct 15, 2013)

  • Fixed bugs in --text.
  • Fixed minor problems related to the new scoring scheme introduced in v7.113.
  • Fixed a minor problem in --text --clustalout.
  • Fixed a minor problem in --nuc --anysymbol.
  • Fixed mistakes in reference alignments in the source package.
  • An experimental option, --similaritylevel f (-1 < f < 1; f=0.0 by default).

New in MAFFT 7.113 (Oct 3, 2013)

  • Changed the default scoring scheme for gaps-rich regions.
  • The quality of large alignment, consisting of 1,000 or more sequences with many gaps, has been improved.
  • Gap-rich regions tend to have more gaps.
  • To disable this change, add the --legacygappenalty option.

New in MAFFT 7.055 (Jul 25, 2013)

  • Changed the calculation procedure of guide tree and sequence weights when empty (or all-gap) sequences are included in the input. This change affects the results only in special cases.
  • Empty sequences are accepted by X-INS-i and Q-INS-i, too.
  • Fixed a potential memory allocation bug in the --treein option.

New in MAFFT 7.053 (Jul 24, 2013)

  • The result of --add has been slightly changed.
  • An experimental option, --addfull.

New in MAFFT 7.050 (Jul 3, 2013)

  • Fixed a bug in the --add option; there was a possibility that repetitive sequences were truncated, when --add was applied without --localpair, --globalpair or --genafpair.
  • This bug affected the --add option in all the previous versions.
  • This bug did not affect the --addfragments or any options other than --add.

New in MAFFT 7.047 (Jul 1, 2013)

  • Updated the --fmodel option, which is for nucleotide alignment with highly biased base composition.

New in MAFFT 7.032 (Apr 22, 2013)

  • Ambiguous nucleotides (r, y, w, s, k, m, d, v, h, b; UIPAC-IUB codes) are scored as:
  • score(r,a) = ( score(a,a) + score(g,a) ) / 2
  • score(r,g) = ( score(a,g) + score(g,g) ) / 2
  • score(r,t) = ( score(a,t) + score(g,t) ) / 2
  • score(r,c) = ( score(a,c) + score(g,c) ) / 2
  • score(r,y) = ( score(r,t) + score(r,c) ) / 2
  • score(r,r) = ( score(a,a) + score(g,g) ) / 2
  • score(y,y) = ( score(c,c) + score(t,t) ) / 2

New in MAFFT 7.031 (Apr 10, 2013)

  • Fixed a bug in handling X in the seed alignment in the --seed option.
  • Improved the efficiency for all-to-all pairwise alignment.

New in MAFFT 7.029 (Mar 15, 2013)

  • Fixed a memory leak.

New in MAFFT 7.027 (Mar 7, 2013)

  • Fixed a memory allocation bug in the --treeout option.
  • Fixed a memory allocation bug in the multithread mode.
  • Fixed a bug in the f2cl program.

New in MAFFT 7.023 (Feb 6, 2013)

  • Improved the efficiency of the --addfragments option for large data. The effect of this change is small in most cases.