MAFFT - a multiple sequence alignment program

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Changelog and bug information Follow @katoh16

v7.520 –

See gitlab for recent changes.

v7.511 2022/12/19

Fixed a bug; Calculation with --adjustdirection could abort when input sequences have long low-complexity region.

v7.510 2022/9/26 (gitlab only)

Adde a new option, --linelength x, to set the length of a line in the FASTA format. x = 60 by default (same as previous versions).
--linelength -1 uses just one line for a sequence.

v7.509 2022/9

Changed some parameters to more reasonable ones in the --textmatrix option.

v7.505 2022/4/10

Added some options for GISAID.
When --maxambiguous is on, successive ns (nucleotide) or Xs (protein) are replaced with a single n or X.

v7.496 2021/12/26

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.

v7.495 2021/12/24

Fixed a bug. When the input data is huge (file size > approx. 2GB), ptrotein data was mis-recognized as DNA. This bug affected the --addfragments option. Online version has been fixed, Dec. 23, 2021. Version 7.495 is available for linux.

v7.490 2021/10/30

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

v7.489 2021/10/23

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

v7.487 2021/7/25

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.

v7.486 2021/7/19

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.

v7.481 2021/5/26

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

v7.480 2021/5/21

Fixed a bug in the MPI mode in version 7.479.

v7.479 2021/5/14

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.

v7.477 2021/2/22

Fixed a compatibility problem in mafft-xinsi with Mac.

v7.474 2020/10/27

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

v7.473 2020/10/23

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.

v7.471 2020/7/3

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.

v7.470 2020/6/20

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

v7.468 2020/6/8

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.

v7.467 2020/5/14

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.

v7.464 2020/4/21

Fixed a bug in version 7.463. Normal options, not for viral genomes, did not work when sequences were long.

v7.463 2020/4/18

Improved memory efficiency of the --addfragments option, when adding many closely-related sequences.

v7.461 2020/4/16 (online only)

The --addfragments option supports larger data, when the input sequences are closely related.

v7.455 2019/12/9

Small change in Makefile to compile and install DASH client smoothly.

v7.450 2019/8/23

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.

v7.429 2019/7/1

Removed an unnecessary line "Active code page: 65001" in output of version 7.428, when running on Windows Command Prompt.
Updated reference results in the test directory in the source package.

v7.428 2019/5/22

Supported folder name containing extended- and non-Latin alphabets in Windows.

v7.427 2019/3/24

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

v7.425 2019/3/20

New option, --dash, to use structural information provided by DASH.

v7.419 2019/1/25

Fixed a bug in the combination of --text and --clustalout.
Fixed a potential problem in hex2maffttext.
Added an experimental option.
Fixed some problems in compiling the source without multithread support.

v7.409 2018/8/22 (Windows only)

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.

v7.408 2018/8/6

Fixed a problem that affected the online version only.

v7.407 2018/7/23

Fixed a problem that occurred when the all-in-one package for Windows was installed in a network folder (\\server\somewhere\mafft-win\).
Supported the interactive mode in the all-in-one packages for Linux and Mac.

v7.402 2018/5/23

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.

v7.396 2018/4/10

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

v7.395 2018/3/17

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

v7.394 2018/3/10

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.

v7.392 2018/3/3

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

v7.390 2018/2/25

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.

v7.387 2018/2/18

Fixed a bug when temporary directory is in Lustre filesystem.

v7.380 2018/1/9

Disabled multithreading in the progressive alignment stage to avoid shortage of stack space, when the number of sequences is large.
Rewrote some of recursive functions as non-recursive ones.
If a UTF-16 or UTF-32 text file is given as input, then exits with an error message.

v7.376 2017/12/20

Revised warnings on Windows, to suggest switching to “Ubuntu on Windows” version.
Updated the maffttext2hex program to support FASTA and CLUSTAL formats.

v7.374 2017/12/16

Fixed a bug in counting the number of physical cores on Windows.
Experimentally released Ubuntu version. Actually linux version also works on Ubuntu on Windows.
In the all-in-one version for Windows, the location of temporary folder has been changed to %TMP% (environmental variable in Windows OS). If it does not work, the location can be changed back by editing the mafft.bat file.

v7.372 2017/12/9

Enhanced the --text mode for non-biological data.

User-defined scoreing matrix, --textmatrix. At most 248 letters can be used instead of 20 amino acids or 4 nucleotides.
Utility for viewing input/output data consisting of extended alphabet.
Utility for preparing input files is not yet provided.

Improved compatibility with Windows.

The number of physical cores is automatically counted with the --thread -1 flag in all-in-one package for Windows, as well as in other packages.
The --reoder option works normally on a wider range of versions of Cygwin.

v7.370 2017/12/6

Enabled iterative refienment in the --add option.

v7.369 2017/12/2

Enabled multithreading for RNA alignment methods (mafft-xinsi and mafft-qinsi) in the cygwin version on Windows.
Fixed a bug in the --text mode; sometimes failed when combined with --globalpair or --localpair.
MPI support for slow progressive options. Detailed document will become available later.

v7.313 2017/11/15

Fixed a bug. When null or empty sequences are included in the input data, calculation of the --add option sometimes failed.

v7.312 2017/10/16

Changed the thresholds for the combination of the --auto option and the --addfragments, --addfull and --addlong options.

2017/5/6

Signed version for Windows (cygwin, all-in-one). Not yet sure how to package signed software.

v7.311 2017/3/28

Fixed a bug in the all-in-one package for Windows. Interactive mode did not work in version 7.310.

v7.310 2017/3/17

Fixed a long-standing problem on exit code.
Fixed version misrecognition on Cygwin 2.7. Pending issue: permission of binary files is sometimes misrecognized on Cygwin.

v7.309 2017/1/26

Fixed minor problems in --progress.

v7.308 2017/1/24

Fixed a bug in the --allowshift option. This bug affected the Windows version only.

v7.307 2017/1/6

Fixed a problem in aligning 'N's in nucleotide sequences in the --allowshift option and the --unalignlevel option.
Fixed a bug in the --merge option in handling >10,000 sequences. The memory usage of this option is still high but will be reduced in future versions.
Fixed incompatibility in the --phylipout option with some versions of PHYLIP.

2016/11/1

A new 64bit package for Windows is in alpha testing. Improved portability. No functional change.

v7.306 2016/8/31

Small changes in an option that is used by the online version only.

2016/8/18

Fixed a bug in the online tree inference service; when the "Allow unusual symbols" option is on and the MSA contains "." (period), the UPGMA program aborted, from mid-Jul to Aug/17. NJ was not affected.

v7.305 2016/8/16

Updated mafft-homologs.rb to use https to access NCBI. Source only.

v7.304 2016/8/12

Fixed a bug; version 7.302 could not be compiled if Makefile was edited to disable multithread.
Fixed an environment-specific bug; on some versions of Cygwin, the --reorder option did not work.

v7.302 2016/8/10

Fixed a bug; the --addfragments and --addlong options sometimes failed (but returned zero), when the input alignment includes very short sequences (2-3 sites excl. gaps).
Fixed a compatibility issue with gcc version 6.1.
Modified some minor features that are used only in the online service.
An experimental option, --nwildcard, for DNA. Expected to be useful when the input data has long stretches of n, where actual sequence is unknown but the length is approximately known.

2016/7/31

Resumed to use twitter.

v7.300 2016/7/31

Fixed a bug in the mafft-sparsecore.rb script; the order of sequences was not as specified in the case of small data.
Fixed several bugs in undocumented options.

v7.299 2016/6/28

Modified a subprogram to estimate the direction of nucleotide sequences in the --adjustdirection and --adjustdirectionaccurately options, to apply them to a larger number of sequences. Still being tested.

v7.295 2016/6/16

Fixed a bug in version 7.294; the --seed option sometimes failed.

v7.294 2016/5/17

Fixed a bug in versions 7.270 - 7.273; the --unweight option did not work in the iterative refinment mode.
In the --localpair, --globalpair and --genafpair options,

slightly reduced the wall-clock time.
slightly improved the accuracy by increasing the precision of numerical calculations related to guide tree.

Added several experimental options.

v7.273 2016/2/20

Improved the efficiency of parallelization when the number of sequences is large and sequence length is short. The FFT-NS-2 and FFT-NS-i options only.

v7.272 2016/2/6

Fixed a bug that the --aamatrix option did not work in versions 7.265 - 7.271.

v7.271 2016/1/7

Fixed a bug in versions 7.265 - 7.270. Option name (FFT-NS-2, etc) displayed at the end of each run was incorrect.

v7.270 2015/12/28

Added several experimental options that will be documented later.
Supported extended alphabet in the --text mode.
Fixed a compatibility problem in mafft-homologs.rb with the newest version of Ruby.
Fixed a problem in the newick2mafft.rb script. When a branch length is 'xe-y', it is interpreted as zero by this version.
Fixed a permission problem in using a temporary folder in the all-in-one version for Windows.

v7.245 2015/07/23

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.

v7.244 2015/06/16 (web and mac)

Changed the parameters for E-INS-i. To disable this change, add the --oldgenarpair option.
Added a new option, --addlong.
(Windows and Linux versions will become available soon.)

v7.236 2015/05/31 (still web version only)

The speed of the --merge option has been improved. This change is effective only when an unrealistic grouping is specified.

v7.233 2015/05/25 (web version only)

Added two new options, --keeplength and --mapout, which work with --add, --addfragments or --addfull.
When iterative refinement options are applied to a large dataset, an error sometimes occurred. This problem has been reduced but not completely solved. The memory requirement has been increased due to this change.

v7.221 2015/04/16

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

v7.220 2015/03/28

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

v7.216 2015/02/28

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

v7.215 2014/12/17

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

v7.213 2014/12/05

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.

v7.212 2014/11/21

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.

v7.205 2014/10/20

Fixed a compilation problem that occurred when multithreading is disabled.

v7.204 2014/10/15

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

v7.187 2014/10/02

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

v7.186 2014/09/29

Fixed an environment-specific bug. On Mac OSX 10.9 (Marvericks), the --progress option did not work.

v7.184 2014/09/21

Experimental support for multithreading on Windows.

v7.182 2014/09/10

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.

v7.164 2014/08/01

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.

v7.158 2014/06/27

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

v7.157 2014/06/10

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.

v7.154 2014/05/17

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.

v7.150 2014/04/28

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

v7.149 2014/04/04

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.

v7.130 2013/12/05

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?

v7.123 2013/10/15

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

v7.122 2013/10/13

Fixed a bug in --text in v7.120. An incorrect scoring matrix was used in the progressive options.
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 (-1.0 ≤ f ≤ 1.0; f=0.0 by default).

v7.120 2013/10/09

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

v7.113 2013/10/01

Changed the default scoring scheme for gap-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.

--legacygappenalty

v7.058 2013/08/04

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

v7.055 2013/07/25

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.

v7.053 2013/07/19

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

2013/07/14

Released a script for regional re-alignment.

v7.051 2013/07/12

Windows version now supports the --quiet mode.
Windows version now ignores the --thread -1 option.
Removed an unnecessary warning.

v7.050 2013/07/03

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.

v7.047 2013/06/24

Updated the --fmodel option for nucleotide alignment with biased base composition.

v7.046 2013/06/12 (source only)

Changed the default compile option of MXSCARNA, such that RNA alignment methods (X-INS-i and Q-INS-i) work more stably in various environments. "-funroll-loops" and "-finline-limit=" have been removed from mafft-*.*-with-extensions/extensions/mxscarna_src/Makefile.

v7.045 2013/06/05

Re-enabled the combination of --merge and --seed.
Fixed a memory leak.

v7.043 2013/05/26

Fixed a bug in the --merge option in the multithread mode in versions 7.036 - 7.040.
Changed the behavior of --merge such that each of the given groups is forced to form a monophyletic cluster.

v7.040 2013/05/20

Enabled iterative refinement in the --merge option.
Disabled the combination of --merge and --seed, because some problems were found.
Changed the order of sequences to reflect the similarity better, when the --reorder --addfragments options are given.

v7.037 2013/04/25

Fixed a bug in the E-INS-i mode in version 7.036.
Fixed a bug in the --clustalout option in version 7.036.

v7.036 2013/04/24

New option: --merge creates a single MSA from multiple sub-MSAs.
Changed the setting of X-INS-i back to that of version 6.864. In versions 6.884 - 7.032, the accuracy of X-INS-i was slightly lower than that of the previous versions.

v7.032 2013/04/14

Ambiguous nucleotides (r, y, w, s, k, m, d, v, h, b; IUPAC-IUB codes) are scored as:
In previous versions, they were scored equivalently to n.

v7.031 2013/04/09

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

v7.029 2013/03/10

Fixed a memory leak.

v7.027 2013/03/07

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.

v7.024 2013/02/21

Support for titles of >10 characters in the phylip format (--phylipout --namelength n). n = 10 by default.
Fixed a bug in the score program.
Slightly changed the format of tree by --dpparttree --treeout and --parttree --treeout.

v7.023 2013/02/03

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

v7.017 2013/01/12

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 version.
Updated references.
Modified the behavior of --auto. The --dpparttree --alga option is selected for large data. There may be further changes in the future.

v7.014 2012/12/17

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.

v7.013 2012/12/15

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

v7.012 2012/12/06

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 ).

v6.956 2012/11/21

The --auto --addfragments option checks the size of problem and automatically determines if an approximate method, --6merpair, is applied. The threshold may be changed in the future.
The --treeout --addfragments option outputs the estimated phylogenetic positions of the sequences to be added.
The --retree 0 --treeout --addfragments option outputs the estimated phylogenetic positions of the sequences to be added. Alignment calculation is skipped.

v6.954, 2012/11/16

Fixed problems in stderr messages.
Modified Makefile such that it strips binaries.
Improved the efficiency of memory usage in the --6merpair --addfragments option.

v6.953, 2012/10/27

Modified the --thread -1 option, such that it correctly counts the number of cores on Linux on VMware.
Corrected an example, test/sample.linsi, in the source package.

v6.952, 2012/10/25

Fixed a bug in --addfragments in version 6.951. If no close relative of a new sequence is found, it ran unstably.
Fixed a problem in indicator of similarity level for nucleotide alignment, in the clustal format.
Extended the length of sequence title, shown in a tree with --treeout, to ∼250 letters.
Improved the efficiency of memory usage in the --6merpair --addfragments option.

v6.951, 2012/10/18

Fixed a bug in the combination of --addfragments and --reorder. The order of sequences in the output was incorrect, in versions 6.923 - 6.950. This bug did not affect the alignment.

v6.950, 2012/10/17

Improved the efficiency of memory usage in the --addfragments option.

v6.940, 2012/10/10

Improved the efficiency of the --addfragments option for a large number of unaligned sequences.

v6.935, 2012/08/21

Improved the parallelization efficiency of the --addfragments for large data. However, for small data, the efficiency has been slightly reduced. The effect of this change is large when applying fast options, --6merpair and --10merpair, to large data, but the effect is small in most cases.
Fixed a memory leak in --addfragments.

v6.927, 2012/08/13

Enabled the --10merpair option for nucleotide alignment. Distance matrix is computed based on the number of shared 10mers.

v6.925, 2012/07/21

Slightly improved the speed of the --addfragments option.

v6.924, 2012/07/19

Fixed a bug in --addfragments when the reference alignment has just one sequence.

v6.923, 2012/07/14

Improved the speed of the --add and --addfragments options when the number of sequences is large.

v6.910, 2012/06/26

Changed the default parameter when calling LAST.

v6.903, 2012/05/24

Fixed several bugs.

v6.901, 2012/05/10

Fixed several bugs.

v6.900, 2012/05/10

Added new options, --adjustdirection and --adjustdirectionaccurately, which adjust the direction of nucleotide sequences, according to the first sequence.

--adjustdirection is based on 6 mer counting and faster.
--adjustdirectionaccurately is based on DP and slower.

Changed the behavior of --thread -1:

# threads := # of physical cores + 1, if hyperthreading is on.
# threads := # of physical cores, if hyperthreading is off.

v6.885, 2012/05/04

A new option, --thread -1, automatically uses an appropriate number of threads (ie, # of threads := # of physical cores). Linux and Mac only.

v6.884, 2012/04/28

A new option, --addfragments, to add short sequences to an existing alignment. The usage and details will be available later.
Experimental support for multithreading on Intel Mac, in addition to Linux.

v6.864m, 2012/03/13

Changed the error message for the case where the MAFFT_BINARIES environmental variable is incorrectly set (Mac only).

v6.864, 2011/11/10

Modified some error messages the main script returns.

v6.861, 2011/10/11

Changed the behavior of the --auto option. When the number of sequences is > 10,000, FFT-NS-1 is selected. FFT-NS-1 is faster than the default (FFT-NS-2).

v6.860, 2011/09/17

Two different group-to-group algorithms, --alga and --algq, are selectable for progressive alignment options, including parttree. The --alga algorithm is a conventional one. The --algq algorithm counts existing gaps differently and the resulting alignment has more gaps.
In this version, by default, --algq is used in the parttree options, --alga is used in the other options.

v6.859, 2011/08/24

Changed the group-to-group alignment algorithm in the --parttree and --dpparttree options, which are for large alignment consisting of 50,000 or more sequences.

The new version tends to generate shorter alignment than previous versions.
According to a benchmark, the previous version is more accurate than the new version. However, the alignment by the previous version sometimes becomes too long.
To emulate previous versions, add --algq

mafft --algq --parttree input > output
mafft --algq --dpparttree input > output

Extended the upper limit of the number of sequences for FFT-NS-1 and FFT-NS-2: 20,000 → 100,000
Extended the upper limit of the number of sequences for iterative refinement options: 4,000 → 6,000

v6.857, 2011/05/30

Fixed a bug in handling very short sequences.
Fixed a memory allocation bug that causes a crash when null sequences are given.
Corrected the default installation directory of mxscarna_mod.

v6.853, 2011/04/27

Fix a bug in the --add option.
Changed the default location of subprograms from /usr/local/lib/mafft/ to /usr/local/libexec/mafft/.

v6.851, 2011/03/30

Fixed incorrect descriptions on the CHECK step in readme.
Modified core/Makefile to be compatible with MacOSX.
(There is no change in binary packages.)

v6.850, 2011/03/05

Corrected a formatting error in the --phylipout option.

v6.849, 2011/02/23

Added the --out option to specify an output file, instead of stdout.
Fixed an incorrect target directory of manpages in Makefile.
Fixed several uninitialized variables and deleted unused variables.

v6.847, 2011/01/12

Beta support for the PHYLIP interleaved format, --phylipout.
Name length n in a CLUSTAL format output can be controlled by --clustalout --namelength n.
Fixed a problem in a newick tree when the --anysymbol and --treeout options are simultaneously set.
Fixed the installation directory of mafft-profile and mafft-distance in Makefile.

v6.846, 2010/12/17

Name length in a tree (generated by --treeout) has been extended from 20 to 60.
Several modifications just for experimental features.

v6.843, 2010/11/29

'U' and other unusual amino acid letters are accepted in the --anysymbol mode.
Upper/lower case is preserved in the --preservecase mode.
Modified Makefile such that the permission of manpages is 644.
Modified the default location of manpages to /usr/local/share/man/man1/.

v6.833, 2010/10/20

Changed the default parameters of mafft-profile.
Faster but more memory demanding for long sequences than previous versions. Use the --memsave option as necessary.

v6.832, 2010/10/07

Fixed a memory allocation bug in FFT-NS-i in the multithreading mode.
Improved the accuracy of long nucleotide alignment.
Fixed a problem of terminal gaps in the --add option.
Extended the upper limit of the number of sequences for iterative refinement option (3,000→4,000).

v6.821, 2010/09/12

Fixed a compatibility problem with CONTRAfold in the RNA alignment mode. This version supports CONTRAfold v2.02.

v6.819, 2010/08/30

Fixed a problem when running on Command Prompt on Windows.

v6.818, 2010/08/16

Fixed a bug in the X-INS-i option on Cygwin.

v6.817, 2010/08/14

Fixed a problem in the --add and --addprofile options when partial sequences are in the existing alignment.
Slightly modified the CUI.

v6.815, 2010/07/21

Fixed a bug in v6.811 - 6.814, in which RNA alignment options (X-INS-i and Q-INS-i) did not work in single-thread mode.

v6.814, 2010/07/13

Slightly modified the CUI.

v6.813, 2010/07/10

Fixed a compatibility problem in the mafft-6.812-win.zip package with 64bit-Windows XP. There may remain the problem with 64bit-Windows VISTA. Cygwin versions do not have this problem.

v6.812, 2010/07/08

Fixed a problem in the mafft-homologs.rb script. In versions ≤6.811, sequence names could be incorrect when used in the server.
All-in-one package that does not require Cygwin on Windows.

v6.811, 2010/05/25

More exact calculation for the --add and --addprofile options.

v6.809, 2010/04/16

The condition for the termination of iterative loop has been modified. The calculation speed was increased, but the efficiency of parallelization was reduced.

v6.806, 2010/02/22

Multithreading (linux only)
A fast option to add sequence(s) to an existing alignment.

v6.717, 2009/12/03

Fixed a problem with directory name containing space.

v6.716, 2009/10/31

Fixed a bug in Makefile of v6.715. If you have the source of v6.715, please replace it with v6.716.
Fixed a platform-specific bug in the mafft script.

v6.715, 2009/10/30

Modified the readme file on how to install without root.

v6.714, 2009/10/19

Approximate distance matrix in the phylip format. mafft-distance -p -i input > output

v6.713, 2009/09/24

Some updates only for the online version.
Changed a stderr message.

v6.712, 2009/09/08

Enabled the combination of --treein and --seed.
Fixed a non-standard usage of fprintf in pairlocalalign.c.

v6.710, 2009/08/24

Fixed an OS-specific bug in --treein. This bug affected the Windows version.

v6.709, 2009/08/18

Fixed non-standard usage of make in extensions/.

v6.708, 2009/07/26

Support for Mac ppc64 and x86_64 binaries.
Modified extensions/Makefile so that it passes down CXX and CXXFLAGS to mxscarna_src. Compilation options can be specified as command-line arguments of make. make CXX="g++" CXXFLAGS="-m32 -fast"

v6.707, 2009/06/01

Fixed a potential overflow problem at the second progressive step of FFT-NS-*.

v6.706, 2009/05/31

Slightly improved performance for alignment of long and highly conserved sequences.

v6.705, 2009/05/16

Re-support for long and highly similar sequences. Versions 6.619-6.704 required a huge RAM space when long (>∼1,000,000) and highly similar sequences were given. To process such sequences with small RAM, the corresponding code was reverted to that of version 6.611.
Corrected a typo in stderr message.

v6.704, 2009/05/07

Support ambiguous amino acid codes, 'Z', 'B', and 'J'. 'U' is not supported.
Fixed a bug in --memsave.

v6.703, 2009/04/28

Fixed a bug in --globalpir --retree 0 --treeout.

v6.626, 2009/03/16

Changed the default setting: --ep 0.123 → --ep 0.0.

v6.624, 2008/12/18

Adjusted parameters of the FFT alignment algorithm, to suppress misalignments such as
TCTA------GGAACGTTAG TCTAGGAACG------TTAG
in an alignment of long genomic DNAs.

v6.621, 2008/12/16

Made minor modifications to input and output formats.
Fixed a bug (v6.500-v6.620) of mafft-xinsi and mafft-qinsi in the --quiet mode.

v6.620, 2008/12/10 6:00 PM JST

Fixed a bug (v6.619) by which L-INS-i, E-INS-i and G-INS-i always abort.

v6.619, 2008/12/10

Enabled L-INS-i, E-INS-i and G-INS-i to handle long sequences (<30,000aa/nt). They may require a huge RAM space.
Fixed a bug (v5-v6.611) at the implementation of the combination of FFT and the memsave mode. This fixation affects the alignments of closely-related and long genomic sequences.
Fixed a bug (v6.605-v6.611) in mafft-homologs.rb.
Fixed some bugs and memory leaks that may be related to a problem that mafft-xinsi --scarnapair sometimes aborts on Windows. This problem is not yet completely solved.

v6.611, 2008/10/23

Changed the distance measures in the *-INS-* strategies. The accuracies of L-INS-i and E-INS-i have been slightly improved, while they have become slightly slow.

v6.608, 2008/09/30

Fixed a bug (v6.605) in mafft-homologs.rb.

v6.605, 2008/09/27

Applied security fixations to the mafft and mafft-homologs.rb scripts, according to the debian team's suggestion.

v6.604, 2008/07/22

Changed compile options of the binary package for Mac.

v6.603, 2008/07/02

Included MXSCARNA (Tabei et al. 2008) for computing pairwise RNA alignment used in X-INS-i.
Modified the LaRA part in the X-INS-i. It depends on a specially adjusted version of LaRA (courtesy of M.Bauer).
Modified PREFIX in Makefile to make it easy to change the default installation directory.

v6.531, 2008/06/02

Fixed a bug in the --treein option.
Disabled the --topin option, because it had a bug.
Added the --averagelinkage and --minimumlinkage options.
The mccaskill routine has become compatible with gcc4.3.

v6.528, 2008/05/27

Fixed some problems in Makefile.
Fixed some problems in interactive mode.
Added an experimental batch script, mafft.bat for Windows.

v6.526, 2008/04/23

Updated mafft-distance.

Accepts short (<6 residues) sequences.
Adopts a length-dependent correction of 6-mer distance (unpublished).

v6.525, 2008/04/05

Fixed a bug at --kappa and --fmodel.

v6.524, 2008/04/04

Added --kimura x and --kappa y. When DNA sequences are aligned, the K80 model (Kimura 1980) with κ = y is used to construct the scoring matrix. Evolutionary distance among the sequences is assumed to be x PAM. Default: --kimura 200 --kappa 2

v6.523, 2008/02/22

Accepts short (<6 residues) sequences.

v6.522, 2008/01/28

Modified the mafft script so that it works with mawk and other awk compatible languages.
The McCaskill-MEA part has become g++4.x compatible.
Reordered the source codes for RNA alignment.

v6.520, 2007/12/23

A new option, X-INS-i, for RNA alignment was added. X-INS-i is a framework based on the Four-way Consistecy objective function to build a multiple structural alignment by combining pairwise structural alignments given by an external program. At present, the external program can be selected from MXSCARNA, LaRA and FOLDALIGN (the local and global options). Although MXSCARNA and LaRA are multiple alignment programs themselves, only their pairwise structural alignment functions are used.

v6.502, 2007/07/30

CONTRAfold (Do et al. 2006) is selectable for calculating RNA base pairing probability. It have to be installed into /usr/local/lib/mafft/.
mafft-qinsi --contrafold

v6.501, 2007/06/12

Fixed bugs in Makefile.

v6.500, 2007/05/23

A new option, Q-INS-i, for RNA alignment was added. It uses a new objective function, Four-way consistency (Katoh and Toh, submitted) calculated from predicted secondary structure.
This version contains codes from McCaskill-MEA and the Vienna RNA package.
C99 compatible (courtesy of D.Mathog)

v6.239, 2007/03/23

Modified messages.

v6.238, 2007/02/18

Fixed a bug in --seed
Changed the default parameter of --dpparttree

v6.236, 2007/02/01

Tree output (all types of guide tree), --treeout

v6.xxx

Group-to-group alignment

Algorithm Q perhaps improves the accuracy of FFT-NS-2, -1 and L-INS-1. We have to do more tests. --algq

Guide tree

A rigorous and fast UPGMA algorithm proposed by Edgar (2004)
An approximate but faster O(N log N) tree-building algorithm (Katoh and Toh; in press), applicable to huge datasets with ~50,000 sequences --parttree or --dpparttree

Evolutionary distance

A length-dependent correction of 6-mer distance has been introduced (unpublished). The accuracy of FFT-NS-1 was greatly enhanced as a result.
Pairwise alignment score, instead of the number of substitutions with the Poisson correction, is used in the second phase of FFT-NS-2 and FFT-NS-i. The effect of this is small in our tests.

misc.

User-defined aa scoring matrix
User-defined aa frequency
--fmodel
Tree output (parttree only)

v5.860, 2006/06/12

The --auto option selects nearly the most accurate method as possible. Not yet tested.

v5.852, 2006/05/20

Support for Mac Universal Binary.
Default of mafft-profile → FFT on
mafft-profile supports memsave.

2006/05/16

Fixed a misdescription of fftnsi in homepage.

v5.851, 2006/05/10

Fixed a bug in mafft-homologs.rb to correctly recognize the version of mafft script.

v5.850, 2006/05/01

v5.830 crashes saying 'hairetsu ga kowareta!' in the memsave mode when inserting a long (>32767) gap. Fixed in v.5.850.
Options for handling a large dataset are automatically chosen in v5.850.
Improved the speed of the FFT part. if( tmpint==0 ) break;

v5.830, 2006/04/24

Version 5.8 can handle larger data than the previous versions (≤5.743). The previous versions aborted with the 'LENGTH OVER' error when the alignment length (incl. gaps) exceeds 5 × the length of the longest input sequence (excl. gaps). This limitation has been removed in ver.5.8. Thus a large dataset (2,000 sequences × 5,000 residues (incl. gaps) or so) can be aligned by the FFT-NS-2 option even when many gaps are needed. See tips for details.
Problems in the memory saving mode have been fixed.

v5.7, 2005/?/?

Version 5.7 has memory saving mode (--memsave) that enables the FFT-NS-x strategies to align long genomic DNA sequences (20kb or more).

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