X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=binaries%2FlinuxIA32%2Fmafft%2Fmafft.1;h=8636334d8ebb4360a8dc13eee02f974ef20f161d;hb=815f71a4a9a91ba271401d5e33ad9ba42cede381;hp=87ac74892a6f3cab83d7b88013b6ec1a4adbdd62;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/binaries/linuxIA32/mafft/mafft.1 b/binaries/linuxIA32/mafft/mafft.1 index 87ac748..8636334 100644 --- a/binaries/linuxIA32/mafft/mafft.1 +++ b/binaries/linuxIA32/mafft/mafft.1 @@ -1,5 +1,5 @@ .\" Title: MAFFT -.\" Author: Kazutaka Katoh +.\" Author: Kazutaka Katoh .\" Generator: DocBook XSL Stylesheets v1.72.0 .\" Date: 2007-08-14 .\" Manual: Mafft Manual @@ -10,8 +10,13 @@ .nh .\" disable justification (adjust text to left margin only) .ad l +.SH "THIS MANUAL IS FOR V6.2XX (2007)" +Recent versions (v6.8xx; 2010 Nov.) have more features than those described below. +See also the tips page at +http://mafft.cbrc.jp/alignment/software/tips0.html .SH "NAME" .RS 0 +.sp mafft \- Multiple alignment program for amino acid or nucleotide sequences .RE .SH "SYNOPSIS" @@ -198,7 +203,7 @@ FASTA is required. Default: off (6mer distance is used) \fB\-\-weighti\fR \fInumber\fR .RS 4 Weighting factor for the consistency term calculated from pairwise alignments. Valid when -either of \-\-blobalpair, \-\-localpair, \-\-genafpair, \-\-fastapair or +either of \-\-globalpair, \-\-localpair, \-\-genafpair, \-\-fastapair or \-\-blastpair is selected. Default: 2.7 .RE .PP @@ -273,7 +278,7 @@ Gap opening penalty at group\-to\-group alignment. Default: 1.53 \fB\-\-ep\fR \fInumber\fR .RS 4 Offset value, which works like gap extension penalty, for -group\-to\-group alignment. Deafult: 0.123 +group\-to\-group alignment. Default: 0.123 .RE .PP \fB\-\-lop\fR \fInumber\fR @@ -331,7 +336,7 @@ the same to that of BLAST. Ignored when nucleotide sequences are input. Defau \fB\-\-fmodel\fR .RS 4 Incorporate the AA/nuc composition information into -the scoring matrix. Deafult: off +the scoring matrix. Default: off .RE .RE .SS "Output" @@ -367,12 +372,12 @@ Do not report progress. Default: off .PP \fB\-\-nuc\fR .RS 4 -Assume the sequences are nucleotide. Deafult: auto +Assume the sequences are nucleotide. Default: auto .RE .PP \fB\-\-amino\fR .RS 4 -Assume the sequences are amino acid. Deafult: auto +Assume the sequences are amino acid. Default: auto .RE .PP \fB\-\-seed\fR \fIalignment1\fR [\fB--seed\fR \fIalignment2\fR \fB--seed\fR \fIalignment3\fR ...] @@ -436,7 +441,7 @@ This variable can be set to indicate to mafft the location to the fasta34 progra .SH "AUTHORS" .RS 0 .PP -\fBKazutaka Katoh\fR <\&katoh_at_bioreg.kyushu\-u.ac.jp\&> +\fBKazutaka Katoh\fR <\&kazutaka.katoh_at_aist.go.jp\&> .sp -1n .IP "" 4 Wrote Mafft.