'\" t
.\"     Title: jaligner
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "JALIGNER" "1" "" "\ \&" "\ \&"
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.SH "NAME"
jaligner \- Smith\-Waterman algorithm with Gotoh\*(Aqs improvement
.SH "SYNOPSIS"
.sp
\f(CRjaligner\fP <s1> <s2> <matrix> <open> <extend>
.sp
Or just type \f(CRjaligner\fP to see the GUI.
.SH "EXAMPLES"
.sp
\f(CRjaligner\fP p53_{human,mouse}.fasta BLOSUM62 10 0.5
.SH "HOMEPAGE"
.sp
.URL "http://jaligner.sourceforge.net/" "" ""