Contents:

BMB - software from the paper:
	K.-M. Chao, R. C. Hardison and W. Miller
	Constrained Sequence Alignment
	Bulletin of Mathematical Biology 55 (1993), 503-524.
TNB - software from the paper
	M. Boguski, R. Hardison, S. Schwartz and W. Miller,
	Analysis of conserved domains and sequence motifs in cellular
	regulatory proteins and locus control regions using new software
	tools for multiple alignment and visualization,
	The New Biologist 4 (1992), 247-260.
band - software from the paper:
	K.-M. Chao, W. Pearson and W. Miller,
	Aligning two sequences within a specified diagonal band,
	CABIOS 8 (1992), 481-487.
blocks - software from the paper:
	W. Miller
	Building multiple alignments from pairwise alignments.
	CABIOS 9 (1993), 169-176.
blocks2 - software from the paper:
	W. Miller, M. Boguski, B. Raghavachari, Z. Zhang and R. Hardison
	Constructing aligned sequence blocks.
	Journal of Computational Biology 1 (1994), 49-61.
chain - software from the paper:
	Z. Zhang, B. Raghavachari, R. Hardison and W. Miller
	Chaining multiple-alignment blocks.
	Journal of Computational Biology 1 (1994), 217-226.
globin - directory for the e-mail server described in
	R. Hardison, K.-M. Chao, S. Schwartz, N. Stojanovic, M. Ganetsy and
		Webb Miller
	Globin Gene Server: a prototype e-mail database server featuring
		extensive multiple alignments and data compilation for
		electronic genetic analysis
	Genomics 21 (1994), 344-353.
falign - software from the paper:
	K.-M. Chao and W. Miller (1994)
	Linear-space algorithms that build local alignments from fragments.
	Algorithmica 13, 106-134.
lat - software for creating PostScript views of yama alignments
new.lav - a more current version of the lav program
old.lav - contains LAV and related programs from the NAR paper:
	S. Schwartz, W. Miller, C.-M. Yang and R. Hardison,
	Software tools for analyzing pairwise alignments of long sequences,
	Nucleic Acids Research 19 (1991), 4663-4667.
robust - software from the paper:
	K.-M. Chao, R. C. Hardison and W. Miller
	Locating well-conserved regions within a pairwise alignment
	CABIOS 9 (1993), 387-396.
sim - contains the SIM and BLAST programs from the NAR paper (see "lav", above)
sim2 - software from the paper:
	K.-M. Chao, J. Zhang, J. Ostell and W. Miller (1994)
	A local alignment tool for very long DNA sequences.
	CABIOS 11 (1995), 147-153.

	More recent and portable versions of this tool can be obtained from
	NCBI.  To obtain a Mac or PC version, send e-mail to:
		zjing@sunset.nlm.nih.gov (Jinghui Zhang)
	To get the sim2 for the UNIX machines, do:
		ftp ncbi.nlm.nih.gov
		login as anonymous
		cd pub/sim2

sim3 - "A tool for aligning very similar DNA sequences",
        Kun-Mao Chao, Jinghui Zhang, James Ostell, and Webb Miller.  
        CABIOS, vol 13, no 1, 1997, pp75--80.

       Available from NCBI, as above.

software.tools - code from Webb's book "A Software Tools Sampler"
software.tools.tar.Z - compressed tar file containing the above
sub - software from the paper:
	Chao, K.-M. (1994)
	Computing all suboptimal alignments in linear space.
	Combinatorial Pattern Matching '94,
	Lecture Notes in Computer Science, 807, 31-42.
yama - software from the papers:
	Hardison, R. C., Chao, K.-M., Adamkiewicz, M., Price, D.,
	Jackson, J., Zeigler, T., Stojanovic, N. and Miller, W. (1993)
	"Positive and negative regulatory elements of the rabbit
 	 embryonic $epsilon$-globin gene revealed by an improved
 	 multiple alignment program and functional analysis"
	DNA Sequence, 4, 163-176.

	Hardison, R. C., Chao, K.-M., Schwartz, S., Ganetsky, M.
	and Miller, W. (1994)
	"Globin Gene Server: A prototype E-mail database sever
 	 featuring extensive multiple alignments and data compilation
 	 for electronic genetic analysis"
	Genomics 21, 344-353.

	Chao, K.-M., Hardison, R. C. and Miller, W. (1994)
	"Recent developments in linear-space alignment methods:
 	 a survey"
	Journal of Computational Biology 1, 271-291.