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MAFFT Changelog

What's new in MAFFT 7.511

Dec 26, 2022
  • Fixed a bug; Calculation with --adjustdirection could abort when input sequences have long low-complexity region.

New in MAFFT 7.496 (Feb 9, 2022)

  • Added a new option, --compactmapout, for handling a large number of sequences in the --addfragments option. Positions of insertions in added sequences are compactly shown in the .map file. This option is being tested online.

New in MAFFT 7.490 (Oct 31, 2021)

  • Fixed a bug in version 7.489, where the X-INS-i and Q-INS-i options did not work depending on environment.

New in MAFFT 7.489 (Oct 25, 2021)

  • Fixed another bug that used more memory than necessary in the FFT-NS-i option in the multithread mode.

New in MAFFT 7.487 (Jul 25, 2021)

  • Fixed a serious bug. In versions 7.463 – 7.486, calculation of the FFT-NS-i option sometimes failed, requesting unnecessarily much memory in the multithread mode. This bug affected the --auto option, too, depending on data size.

New in MAFFT 7.486 (Jul 20, 2021)

  • A combination of --allowshift and --treein treefile can be used to give expected similarity level, using the branch lengths in the tree. If the input data has regions that are less similar than the assumption, then the regions are unaligned. This combination of options worked in versions ≤7.481, too, but the given tree was used only as a guide tree, not to specify the expected similarity level.

New in MAFFT 7.481 (Jun 1, 2021)

  • Changed the permission of progress file (set by --progress filename) to system default.

New in MAFFT 7.479 (May 14, 2021)

  • Fixed a bug in a combination of zero gap open cost (--op 0 --gop 0) and user-defined scoring matrix (--aamatrix or --textmatrix).
  • Extended the upper limit of input sequences to the --dash option from 750 to 3000.

New in MAFFT 7.475 (Nov 23, 2020)

  • Fixed a bug in version 7.473; the --anysymbol option did not work with the --maxambiguous x option.

New in MAFFT 7.473 (Nov 23, 2020)

  • Added a new option, --maxambiguous x. If the frequency of ambiguous bases/amino acids in a sequence is greater than x (0≤x≤1.0), then the sequence is removed. This is option is enabled by default only in the online version of addfragments.
  • Improved the efficiency of memory usage when applying the --addfragments option to small size data.

New in MAFFT 7.471 (Jul 3, 2020)

  • Fixed a problem in the --addfragments option. When the input data had many all-gap sites, the calculation did not start. Versions 7.468 and 7.470 had this problem.

New in MAFFT 7.470 (Jul 3, 2020)

  • Fixed a serious bug. When input filename contains *n-n*, calculation stopped. This bug affected versions 7.396 – 7.468.

New in MAFFT 7.468 (Jul 3, 2020)

  • Exits if the reference MSA (or sequence) has too many ambiguous sites, in the --addfragments option. Threshold is tentatively 3%, but may become adjustable in the future.

New in MAFFT 7.467 (May 14, 2020)

  • Fixed a problem (considerable slowdown) when adding many closely-related sequences to a reference MSA consisting of > 1000 sequences.
  • In the --dash option, structural information was not included when input sequences have gap. Fixed this problem.
  • Fixed some (not all) potential problems in compatibility with gcc 8.

New in MAFFT 7.464 (May 11, 2020)

  • Fixed a bug in version 7.463. Normal options, not for viral genomes, did not work when sequences were long.
  • Improved memory efficiency of the --addfragments option, when adding many closely-related sequences.
  • The --addfragments option supports larger data, when the input sequences are closely related.
  • Small change in Makefile to compile and install DASH client smoothly.

New in MAFFT 7.450 (Apr 18, 2020)

  • Fixed a problem in --dash. The original sequences were not included in the output in a small number of cases.
  • When the --adjustdirections flag is applied to RNA sequences (incl. u), a is flipped to u, instead of t.
  • Experimental support for multiple alignment of error-prone reads using LAST and MAFFT.

New in MAFFT 7.429 (Jun 29, 2019)

  • Removed an unnecessary line "Active code page: 65001" in output of version 7.428, when running on Windows Command Prompt.

New in MAFFT 7.428 (May 22, 2019)

  • Fixed a bug in --dash. :
  • This option incorrectlry worked in the single thread mode in v7.425 (released 2019/Mar/20).

New in MAFFT 7.427 (Mar 24, 2019)

  • Fixed a bug in --dash. This option incorrectlry worked in the single thread mode in v7.425

New in MAFFT 7.409 (Aug 22, 2018)

  • Fixed a problem in the all-in-one package for Windows of version 7.407 (released 2018/Jul). This problem might affect GUI programs that internally run MAFFT on Windows.
  • When the mafft.bat script ran on Command Pormpt and output file was specified after >, ie, mafft.bat input > output
  • an unnecessary single-byte character was inserted at the head of the output file.

New in MAFFT 7.408 (Aug 22, 2018)

  • Fixed a problem that affected the online version only.

New in MAFFT 7.407 (Jul 23, 2018)

  • Fixed a problem that occurred when the all-in-one package for Windows was installed in a network folder (\serversomewheremafft-win).

New in MAFFT 7.402 (May 23, 2018)

  • Fixed a bug in the --merge option in versions 7.307 – 7.396. Sometimes failed when given grouping was inconsistent with internally estimated grouping.
  • Results of G-INS-i and G-INS-1 options have been changed slightly.

New in MAFFT 7.396 (Apr 16, 2018)

  • Fixed a problem in versions 7.380 – 7.395; an unnecessary warning was shown depending on input file name.

New in MAFFT 7.395 (Mar 19, 2018)

  • Fixed a problem that occurred when the temporary directory is set by the MAFFT_TMPDIR environmental variable and the directory name has space(s).

New in MAFFT 7.394 (Mar 19, 2018)

  • Fixed a bug in versions 7.380 – 7.392. Due to this bug:
  • The --add option sometimes failed when combined with --localpair, --globalpair or --genafpair.
  • The --merge option sometimes failed in the multithread mode.

New in MAFFT 7.392 (Mar 19, 2018)

  • Fixed a problem in the --auto mode when combined with --merge, --addfragments, etc.

New in MAFFT 7.390 (Mar 19, 2018)

  • Fixed bugs in Makefile.
  • Updated the mafft-profile program for large numbers of sequences (>1,000,000).
  • % mafft-profile -u -N msa1 msa2
  • Added the hex2maffttext program for comparing texts composed of at most 248 alphabets.

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 (Feb 28, 2015)

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

New in MAFFT 7.215 (Feb 28, 2015)

  • 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 7.214 (Dec 15, 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 5, 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 (Nov 24, 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 occurred due to this bug.

New in MAFFT 7.205f (Nov 22, 2014)

  • Version 7.205f experimentally supports multithreading

New in MAFFT 7.205 (Oct 20, 2014)

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

New in MAFFT 7.204 (Oct 20, 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 7.184 (Sep 23, 2014)

  • Experimental support for multithreading on Windows.

New in MAFFT 7.183 (Sep 22, 2014)

  • Experimental support for multithreading on Windows.

New in MAFFT 7.182 (Sep 22, 2014)

  • Thresholds to switch strategies (L-INS-i, FFT-NS-2, etc) in the --auto mode have been changed again.
  • Improved the speed of the FFT-NS-2 option (∼40% when the number of sequences is ∼10,000).
  • Fixed a bug in the combination of --seed and --anysymbol. Due to this bug, unnecessary texts had been added to title lines.

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 27, 2014)

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

New in MAFFT 7.157 (Jun 10, 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 7.130 (Dec 11, 2013)

  • 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 (Dec 11, 2013)

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

New in MAFFT 7.122 (Oct 14, 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.
  • An experimental option, --similaritylevel f (-1 < f < 1; f=0.0 by default).

New in MAFFT 7.120 (Oct 14, 2013)

  • An experimental option for non-biological sequence comparison, --text

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 7.058b (Aug 16, 2013)

  • Modified core/Makefile such that it passes $LDFLAGS to comiler.
  • Fixed a potential problem in interpreting comannd-line arguments in C subprograms.

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 when used in regional re-alignment.
  • 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 7.032 (Apr 25, 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
  • ...
  • In previous versions, they were scored equivalently to n.

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 7.023b (Feb 6, 2013)

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

New in MAFFT 7.017 (Feb 6, 2013)

  • Fixed a Windows-specific bug; incorrect option name was displayed at the end of calculation in versions 7.012-7.015.
  • Changed some features only used in the web service.
  • Updated references.
  • Modified the behavior of --auto. The --dpparttree --alga option is selected for large data. There may be further changes in the future.

New in MAFFT 7.014 (Feb 6, 2013)

  • Fixed a problem that the order of sequences (with the --reorder option) was slightly different from the order of sequences in the guide tree (--treeout), in the FFT-NS-i option.

New in MAFFT 7.013 (Feb 6, 2013)

  • Changed an output format that is only used internally in the web service.
  • This version uses local alignment to estimate the direction of nucleotide sequences, in the --adjustdirectionaccurately option.

New in MAFFT 7.012 (Feb 6, 2013)

  • Modified the behavior of --auto --addfragments. The thresholds may be changed in the future.
  • The number of threads for the iterative refinment stage can be specified by --threadit n, independently from --thread m. By default, n = min( 6, m ).