*** Notice that a newer version is under development. ***

This package contains the following files:

README
list.h
db_list.h
lslist.c
ldb_slist.c
falign.c
falignMake

g_any.c
ftor_rec.c
ftorMake


To compile:

Type "make -f falignMake" for making the execution file `falign'
Type "make -f ftorMake" for making the execution file `ftor_rec'


Usage:

1. To generate fragments:
	falign K seq1 seq2 ...
	(r: replacement cost; o: gap-open; e: gap-extension; W: fragment size)
	e.g. falign 200 human.seq rabbit.seq r=0.1 o=3.0 e=0.2 W=8 > falign.8

2. To refine fragments by running the constrained alignment program:
	ftor_rec frag_out mismatch gap-open gap-ext
	e.g. ftor_rec falign.8 -1 4.0 0.4 > out.8

3. A combined usage:
	falign 200 human.seq rabbit.seq r=0.1 o=3.0 e=0.2 W=8 | ftor_rec -1 4.0 0.4 > out.8