+++ /dev/null
-<html><head>\r
-<meta http-equiv="content-type" content="text/html; charset=ISO-8859-1"><title>Manpage of MAFFT</title>\r
-<link rel="stylesheet" type="text/css" href="mafft_manual_files/tt.css">\r
-</head><body>\r
-<h1>MAFFT</h1>\r
-Section: Mafft Manual (1)<br>Updated: 2007-06-09<br><a href="#index">Index</a>\r
-<a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Return to Main Contents</a><hr>\r
-\r
-\r
-\r
-\r
-\r
-<a name="lbAB"> </a>\r
-<h2>NAME</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-mafft - Multiple alignment program for amino acid or nucleotide sequences\r
-</dd></dl>\r
-\r
-<a name="lbAC"> </a>\r
-<h2>SYNOPSIS</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> [<b>options</b>] <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>linsi</b> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>ginsi</b> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>einsi</b> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>fftnsi</b> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>fftns</b> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>nwns</b> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>nwnsi</b> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>mafft-profile</b> <i>group1</i> <i>group2</i> [> <i>output</i>]\r
-</dt><dt>\r
-<p>\r
-<i>input</i>, <i>group1</i> and <i>group2</i> must be in FASTA format.\r
-</p></dt></dl>\r
-</dd></dl>\r
-\r
-<a name="lbAD"> </a>\r
-<h2>DESCRIPTION</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<b>MAFFT</b> is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods.\r
-</dd></dl>\r
-<a name="lbAE"> </a>\r
-<h3>Accuracy-oriented methods:</h3>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*L-INS-i (probably most accurate; recommended for <200 sequences;\r
-iterative refinement method incorporating local pairwise alignment\r
-information):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--localpair</b> <b>--maxiterate</b> <i>1000</i> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>linsi</b> <i>input</i> [> <i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>*G-INS-i (suitable for sequences\r
-of similar lengths; recommended for <200 sequences; iterative\r
-refinement method incorporating global pairwise alignment information):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--globalpair</b> <b>--maxiterate</b> <i>1000</i> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>ginsi</b> <i>input</i> [> <i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--ep</b> <i>0</i> <b>--genafpair</b> <b>--maxiterate</b> <i>1000</i> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>einsi</b> <i>input</i> [> <i>output</i>]\r
-</dt><dd>\r
-<p>\r
-</p></dd><dd>For E-INS-i, the\r
-<b>--ep</b>\r
-<i>0</i>\r
-option is recommended to allow large gaps.\r
-</dd></dl>\r
-</dd></dl>\r
-\r
-<a name="lbAF"> </a>\r
-<h3>Speed-oriented methods:</h3>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*FFT-NS-i (iterative refinement method; two cycles only):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b> <i>2</i> <b>--maxiterate</b> <i>2</i> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>fftnsi</b> <i>input</i> [> <i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*FFT-NS-i (iterative refinement method; max. 1000 iterations):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b> <i>2</i> <b>--maxiterate</b> <i>1000</i> <i>input</i> [> <i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*FFT-NS-2 (fast; progressive method):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b> <i>2</i> <b>--maxiterate</b> <i>0</i> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>fftns</b> <i>input</i> [> <i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b> <i>1</i> <b>--maxiterate</b> <i>0</i> <i>input</i> [> <i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*NW-NS-i (iterative refinement method without FFT approximation; two cycles only):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b> <i>2</i> <b>--maxiterate</b> <i>2</i> <b>--nofft</b> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>nwnsi</b> <i>input</i> [> <i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*NW-NS-2 (fast; progressive method without the FFT approximation):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b> <i>2</i> <b>--maxiterate</b> <i>0</i> <b>--nofft</b> <i>input</i> [> <i>output</i>]\r
-</dt><dt>\r
-<b>nwns</b> <i>input</i> [> <i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):\r
-<dl compact="compact">\r
-<dt>\r
-<b>mafft</b> <b>--retree</b> <i>1</i> <b>--maxiterate</b> <i>0</i> <b>--nofft</b> <b>--parttree</b> <i>input</i> [> <i>output</i>]\r
-</dt></dl>\r
-</dd></dl>\r
-\r
-<a name="lbAG"> </a>\r
-<h3>Group-to-group alignments</h3>\r
-\r
-<dl compact="compact">\r
-<dt>\r
-</dt><dl compact="compact"><dt></dt><dd>\r
-<b>mafft-profile</b> <i>group1</i> <i>group2</i> [> <i>output</i>]\r
-<p>\r
-</p></dd><dd>or:\r
-<p>\r
-<b>mafft</b> <b>--maxiterate</b> <i>1000</i> <b>--seed</b> <i>group1</i> <b>--seed</b> <i>group2</i> /dev/null [> <i>output</i>]\r
-</p></dd></dl>\r
-\r
-\r
-\r
-</dl>\r
-<a name="lbAH"> </a>\r
-<h2>OPTIONS</h2>\r
-\r
-<a name="lbAI"> </a>\r
-<h3>Algorithm</h3>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>--auto</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data \r
-size. Default: off (always FFT-NS-2)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--6merpair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Distance is calculated based on the number of shared 6mers. Default: on\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--globalpair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-All pairwise alignments are computed with the Needleman-Wunsch\r
-algorithm. More accurate but slower \r
-than --6merpair. Suitable for a set of\r
-globally alignable sequences. Applicable to \r
-up to ~200 sequences. A combination with --maxiterate 1000 is recommended (G-INS-i). Default: off (6mer distance is used)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--localpair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-All pairwise alignments are computed with the Smith-Waterman\r
-algorithm. More accurate but slower\r
-than --6merpair. Suitable for a set of \r
-locally alignable sequences. Applicable to \r
-up to ~200 sequences. A combination with --maxiterate 1000 is recommended (L-INS-i). Default: off (6mer distance is used)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--genafpair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-All pairwise alignments are computed with a local\r
-algorithm with the generalized affine gap cost\r
-(Altschul 1998). More accurate but slower\r
-than --6merpair. Suitable when large internal gaps\r
-are expected. Applicable to \r
-up to ~200 sequences. A combination with --maxiterate 1000 is recommended (E-INS-i). Default: off (6mer distance is used)\r
-</dd></dl>\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-<p>\r
-\r
-<b>--fastapair</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-All pairwise alignments are computed with FASTA (Pearson and Lipman 1988).\r
-FASTA is required. Default: off (6mer distance is used)\r
-</dd></dl>\r
-\r
-\r
-\r
-\r
-\r
-\r
-\r
-<p>\r
-\r
-<b>--weighti</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Weighting factor for the consistency term calculated from pairwise alignments. Valid when \r
-either of --blobalpair, --localpair, --genafpair, --fastapair or \r
---blastpair is selected. Default: 2.7\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--retree</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Guide tree is built <i>number</i> times in the \r
-progressive stage. Valid with 6mer distance. Default: 2\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--maxiterate</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-<i>number</i> cycles of iterative refinement are performed. Default: 0\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--fft</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Use FFT approximation in group-to-group alignment. Default: on\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--nofft</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Do not use FFT approximation in group-to-group alignment. Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--noscore</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Alignment score is not checked in the iterative refinement stage. Default: off (score is checked)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--memsave</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Use the Myers-Miller (1988) algorithm. Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt).\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--parttree</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Use a fast tree-building method (PartTree, Katoh and Toh 2007) with\r
-the 6mer distance. Recommended for a large number (> ~10,000) \r
-of sequences are input. Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--dpparttree</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-The PartTree algorithm is used with distances based on DP. Slightly\r
-more accurate and slower than --parttree. Recommended for a large\r
-number (> ~10,000) of sequences are input. Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--fastaparttree</b>\r
-</p><dl compact="compact"><dt></dt><dd>The PartTree algorithm is used\r
-with distances based on FASTA. Slightly more accurate and slower than\r
---parttree. Recommended for a large number (> ~10,000) of sequences\r
-are input. FASTA is required. Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--partsize</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-The number of partitions in the PartTree algorithm. Default: 50\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--groupsize</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Do not make alignment larger than <i>number</i> sequences. Valid only with the --*parttree options. Default: the number of input sequences\r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAJ"> </a>\r
-<h3>Parameter</h3>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>--op</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap opening penalty at group-to-group alignment. Default: 1.53\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--ep</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Offset value, which works like gap extension penalty, for\r
-group-to-group alignment. Deafult: 0.123\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--lop</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap opening penalty at local pairwise \r
-alignment. Valid when\r
-the --localpair or --genafpair option is selected. Default: -2.00\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--lep</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Offset value at local pairwise alignment. Valid when\r
-the --localpair or --genafpair option is selected. Default: 0.1\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--lexp</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap extension penalty at local pairwise alignment. Valid when\r
-the --localpair or --genafpair option is selected. Default: -0.1\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--LOP</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap opening penalty to skip the alignment. Valid when the\r
---genafpair option is selected. Default: -6.00\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--LEXP</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Gap extension penalty to skip the alignment. Valid when the\r
---genafpair option is selected. Default: 0.00\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--bl</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-BLOSUM <i>number</i> matrix (Henikoff and Henikoff 1992) is used. <i>number</i>=30, 45, 62 or 80. Default: 62\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--jtt</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-JTT PAM <i>number</i> (Jones et al. 1992) matrix is used. <i>number</i>>0. Default: BLOSUM62\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--tm</b> <i>number</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Transmembrane PAM <i>number</i> (Jones et al. 1994) matrix is used. <i>number</i>>0. Default: BLOSUM62\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--aamatrix</b> <i>matrixfile</i>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Use a user-defined AA scoring matrix. The format of <i>matrixfile</i> is\r
-the same to that of BLAST. Ignored when nucleotide sequences are input. Default: BLOSUM62\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--fmodel</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Incorporate the AA/nuc composition information into\r
-the scoring matrix. Deafult: off\r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAK"> </a>\r
-<h3>Output</h3>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>--clustalout</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Output format: clustal format. Default: off (fasta format)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--inputorder</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Output order: same as input. Default: on\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--reorder</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Output order: aligned. Default: off (inputorder)\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--treeout</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Guide tree is output to the <i>input</i>.tree file. Default: off\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--quiet</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Do not report progress. Default: off\r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAL"> </a>\r
-<h3>Input</h3>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>--nuc</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Assume the sequences are nucleotide. Deafult: auto\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--amino</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Assume the sequences are amino acid. Deafult: auto\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>--seed</b> <i>alignment1</i> [<b>--seed</b> <i>alignment2</i> <b>--seed</b> <i>alignment3</i> ...]\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Seed alignments given in <i>alignment_n</i> (fasta format) are aligned with \r
-sequences in <i>input</i>. The alignment within every seed is preserved. \r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAM"> </a>\r
-<h2>FILES</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-Mafft stores the input sequences and other files in a temporary directory, which by default is located in\r
-<i>/tmp</i>.\r
-</p></dd></dl>\r
-\r
-<a name="lbAN"> </a>\r
-<h2>ENVIONMENT</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>MAFFT_BINARIES</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-Indicates the location of the binary files used by mafft. By default, they are searched in\r
-<i>/usr/local/lib/mafft</i>, but on Debian systems, they are searched in\r
-<i>/usr/lib/mafft</i>.\r
-</dd></dl>\r
-\r
-<p>\r
-\r
-<b>FASTA_4_MAFFT</b>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH.\r
-</dd></dl>\r
-\r
-</dd></dl>\r
-\r
-<a name="lbAO"> </a>\r
-<h2>SEE ALSO</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-</p><p>\r
-<b><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/manual/mafft-homologs2.1.html">mafft-homologs</a></b>(1)\r
-</p></dd></dl>\r
-\r
-<a name="lbAP"> </a>\r
-<h2>REFERENCES</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-</dd></dl>\r
-<a name="lbAQ"> </a>\r
-<h3>In English</h3>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>*Katoh and Toh (Bioinformatics\r
-23:372-374, 2007) PartTree: an algorithm to build an approximate tree\r
-from a large number of unaligned sequences (describes the PartTree\r
-algorithm).\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>*Katoh, Kuma, Toh and Miyata\r
-(Nucleic Acids Res. 33:511-518, 2005) MAFFT version 5: improvement in\r
-accuracy of multiple sequence alignment (describes [ancestral versions\r
-of] the G-INS-i, L-INS-i and E-INS-i strategies)\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>*Katoh, Misawa, Kuma and Miyata\r
-(Nucleic Acids Res. 30:3059-3066, 2002) MAFFT: a novel method for rapid\r
-multiple sequence alignment based on fast Fourier transform (describes\r
-the FFT-NS-1, FFT-NS-2 and FFT-NS-i strategies)\r
-</dd></dl>\r
-\r
-<a name="lbAR"> </a>\r
-<h3>In Japanese</h3>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*Katoh and Misawa (Seibutsubutsuri 46:312-317, 2006) Multiple Sequence Alignments: the Next Generation\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
-*Katoh and Kuma (Kagaku to Seibutsu 44:102-108, 2006) Jissen-teki Multiple Alignment\r
-</dd></dl>\r
-\r
-\r
-<a name="lbAS"> </a>\r
-<h2>AUTHORS</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-<p>\r
-\r
-<b>Kazutaka Katoh</b> <katoh_at_bioreg.kyushu-u.ac.jp>\r
-</p><p>\r
-</p><dl compact="compact">\r
-<dt></dt><dd>\r
-Wrote Mafft.\r
-</dd></dl>\r
-<p>\r
-\r
-<b>Charles Plessy</b> <charles-debian-nospam_at_plessy.org>\r
-</p><p>\r
-</p><dl compact="compact">\r
-<dt></dt><dd>\r
-Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.\r
-</dd></dl>\r
-</dd></dl>\r
-\r
-<a name="lbAT"> </a>\r
-<h2>COPYRIGHT</h2>\r
-\r
-<dl compact="compact"><dt></dt><dd>\r
-Copyright © 2002-2007 Kazutaka Katoh (mafft)\r
-<br>\r
-\r
-Copyright © 2007 Charles Plessy (this manpage)\r
-<br>\r
-\r
-<p>\r
-\r
-Mafft and its manpage are offered under the following conditions:\r
-</p><p>Redistribution and use in source and binary forms, with or\r
-without modification, are permitted provided that the following\r
-conditions are met:\r
-</p><p>\r
-</p><dl compact="compact"><dt></dt><dd>\r
- 1.Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd> 2.Redistributions in binary\r
-form must reproduce the above copyright notice, this list of conditions\r
-and the following disclaimer in the documentation and/or other\r
-materials provided with the distribution.\r
-</dd></dl>\r
-\r
-<p>\r
-</p><dl compact="compact"><dt></dt><dd> 3.The name of the author may\r
-not be used to endorse or promote products derived from this software\r
-without specific prior written permission.\r
-</dd></dl>\r
-\r
-<p>THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR\r
-IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED\r
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\r
-DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,\r
-INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES\r
-(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\r
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)\r
-HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,\r
-STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING\r
-IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE\r
-POSSIBILITY OF SUCH DAMAGE.\r
-<br>\r
-\r
-</p></dd></dl>\r
-\r
-<p>\r
-\r
-</p><hr>\r
-<a name="index"> </a><h2>Index</h2>\r
-<dl>\r
-<dt><a href="#lbAB">NAME</a></dt><dd>\r
-</dd><dt><a href="#lbAC">SYNOPSIS</a></dt><dd>\r
-</dd><dt><a href="#lbAD">DESCRIPTION</a></dt><dd>\r
-<dl>\r
-<dt><a href="#lbAE">Accuracy-oriented methods:</a></dt><dd>\r
-</dd><dt><a href="#lbAF">Speed-oriented methods:</a></dt><dd>\r
-</dd><dt><a href="#lbAG">Group-to-group alignments</a></dt><dd>\r
-</dd></dl>\r
-</dd><dt><a href="#lbAH">OPTIONS</a></dt><dd>\r
-<dl>\r
-<dt><a href="#lbAI">Algorithm</a></dt><dd>\r
-</dd><dt><a href="#lbAJ">Parameter</a></dt><dd>\r
-</dd><dt><a href="#lbAK">Output</a></dt><dd>\r
-</dd><dt><a href="#lbAL">Input</a></dt><dd>\r
-</dd></dl>\r
-</dd><dt><a href="#lbAM">FILES</a></dt><dd>\r
-</dd><dt><a href="#lbAN">ENVIONMENT</a></dt><dd>\r
-</dd><dt><a href="#lbAO">SEE ALSO</a></dt><dd>\r
-</dd><dt><a href="#lbAP">REFERENCES</a></dt><dd>\r
-<dl>\r
-<dt><a href="#lbAQ">In English</a></dt><dd>\r
-</dd><dt><a href="#lbAR">In Japanese</a></dt><dd>\r
-</dd></dl>\r
-</dd><dt><a href="#lbAS">AUTHORS</a></dt><dd>\r
-</dd><dt><a href="#lbAT">COPYRIGHT</a></dt><dd>\r
-</dd></dl>\r
-<hr>\r
-This document was created by\r
-man2html,\r
-using the manual pages.<br>\r
-Time: 02:26:04 GMT, August 14, 2007\r
-</body></html>
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