New Mafft binaries for 32 bit linux system

[jabaws.git] / binaries / linuxIA32 / mafft / mafft.1

diff --git a/binaries/linuxIA32/mafft/mafft.1 b/binaries/linuxIA32/mafft/mafft.1
index 87ac748..8636334 100644 (file)
--- a/binaries/linuxIA32/mafft/mafft.1
+++ b/binaries/linuxIA32/mafft/mafft.1
@@ -1,5 +1,5 @@
 .\"     Title: MAFFT
-.\"    Author: Kazutaka Katoh <katoh_at_bioreg.kyushu-u.ac.jp.>
+.\"    Author: Kazutaka Katoh <kazutaka.katoh@aist.go.jp>
 .\" Generator: DocBook XSL Stylesheets v1.72.0 <http://docbook.sf.net/>
 .\"      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.