diff options
Diffstat (limited to 'academic/mafft')
| -rw-r--r-- | academic/mafft/References | 70 | ||||
| -rw-r--r-- | academic/mafft/mafft.SlackBuild | 2 | ||||
| -rw-r--r-- | academic/mafft/mafft.info | 6 |
3 files changed, 39 insertions, 39 deletions
diff --git a/academic/mafft/References b/academic/mafft/References index 62541ce9e8..3ec3ebe6ac 100644 --- a/academic/mafft/References +++ b/academic/mafft/References @@ -1,35 +1,35 @@ -- Katoh, Frith 2012 (Bioinformatics Advance Access) - Adding unaligned sequences into an existing alignment using MAFFT - and LAST. - (describes the --add and --addfragments options) -- Katoh, Toh 2010 (Bioinformatics 26:1899-1900) - Parallelization of the MAFFT multiple sequence alignment program. - (describes the multithread version) -- Katoh, Asimenos, Toh 2009 (Methods in Molecular Biology 537:39-64) - Multiple Alignment of DNA Sequences with MAFFT. In Bioinformatics - for DNA Sequence Analysis edited by D. Posada - (outlines DNA alignment methods and several tips including - group-to-group alignment and rough clustering of a large - number of sequences) -- Katoh, Toh 2008 (BMC Bioinformatics 9:212) - Improved accuracy of multiple ncRNA alignment by incorporating - structural information into a MAFFT-based framework. - (describes RNA structural alignment methods) -- Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298) - Recent developments in the MAFFT multiple sequence alignment - program. - (outlines version 6; Fast Breaking Paper in Thomson Reuters' - ScienceWatch) -- Katoh, Toh 2007 (Bioinformatics 23:372-374) Errata - PartTree: an algorithm to build an approximate tree from a large - number of unaligned sequences. - (describes the PartTree algorithm) -- Katoh, Kuma, Toh, Miyata 2005 (Nucleic Acids Res. 33:511-518) - MAFFT version 5: improvement in accuracy of multiple sequence - alignment. - (describes [ancestral versions of] the G-INS-i, L-INS-i and - E-INS-i strategies) -- Katoh, Misawa, Kuma, Miyata 2002 (Nucleic Acids Res. 30:3059-3066) - MAFFT: a novel method for rapid multiple sequence alignment based - on fast Fourier transform. - (describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies) +Katoh, Standley 2013 (Molecular Biology and Evolution 30:772-780) +MAFFT multiple sequence alignment software version 7: improvements in performance and usability. +(outlines version 7) + +Katoh, Frith 2012 (Bioinformatics 28:3144-3146) +Adding unaligned sequences into an existing alignment using MAFFT and LAST. +(describes the --add and --addfragments options) + +Katoh, Toh 2010 (Bioinformatics 26:1899-1900) +Parallelization of the MAFFT multiple sequence alignment program. +(describes the multithread version) + +Katoh, Asimenos, Toh 2009 (Methods in Molecular Biology 537:39-64) +Multiple Alignment of DNA Sequences with MAFFT. In Bioinformatics for DNA Sequence Analysis edited by D. Posada +(outlines DNA alignment methods and several tips including group-to-group alignment and rough clustering of a large number of sequences) + +Katoh, Toh 2008 (BMC Bioinformatics 9:212) +Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework. +(describes RNA structural alignment methods) + +Katoh, Toh 2008 (Briefings in Bioinformatics 9:286-298) +Recent developments in the MAFFT multiple sequence alignment program. +(outlines version 6; Fast Breaking Paper in Thomson Reuters' ScienceWatch) + +Katoh, Toh 2007 (Bioinformatics 23:372-374) Errata +PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. +(describes the PartTree algorithm) + +Katoh, Kuma, Toh, Miyata 2005 (Nucleic Acids Res. 33:511-518) +MAFFT version 5: improvement in accuracy of multiple sequence alignment. +(describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies) + +Katoh, Misawa, Kuma, Miyata 2002 (Nucleic Acids Res. 30:3059-3066) +MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. +(describes the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies) diff --git a/academic/mafft/mafft.SlackBuild b/academic/mafft/mafft.SlackBuild index 9dee798f39..c39e568aa3 100644 --- a/academic/mafft/mafft.SlackBuild +++ b/academic/mafft/mafft.SlackBuild @@ -23,7 +23,7 @@ # ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=mafft -VERSION=${VERSION:-6.953} +VERSION=${VERSION:-7.037} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} diff --git a/academic/mafft/mafft.info b/academic/mafft/mafft.info index d72e1f0e90..5885262d21 100644 --- a/academic/mafft/mafft.info +++ b/academic/mafft/mafft.info @@ -1,8 +1,8 @@ PRGNAM="mafft" -VERSION="6.953" +VERSION="7.037" HOMEPAGE="http://mafft.cbrc.jp/alignment/software/" -DOWNLOAD="http://mafft.cbrc.jp/alignment/software/mafft-6.953-with-extensions-src.tgz" -MD5SUM="5ce2e3c5b97fb86aac90262191d61df3" +DOWNLOAD="http://mafft.cbrc.jp/alignment/software/mafft-7.037-with-extensions-src.tgz" +MD5SUM="dfa90adaff82e6819458ecbacb96e27b" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" |