Software for computational molecular biology

lav - LAV and related programs from the paper:

S. Schwartz, W. Miller, C.-M. Yang and R. C. Hardison (1991) Software tools for analyzing pairwise alignments of long sequences. Nucleic Acids Research 19, 4663-4667.

sim - the SIM and BLAST programs from the above paper

tnb - from the paper:

M. Boguski, R. C. Hardison, S. Schwartz and W. Miller (1992) 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, 247-260.

band - from the paper:

K.-M. Chao, W. Pearson and W. Miller (1992) Aligning two sequences within a specified diagonal band. CABIOS 8, 481-487.

bmb - from the paper:

K.-M. Chao, R. C. Hardison and W. Miller (1993) Constrained sequence alignment. Bulletin of Mathematical Biology 55, 503-524.

blocks - from the paper:

W. Miller (1993) Building multiple alignments from pairwise alignments. CABIOS 9, 169-176.

blocks2 - from the paper:

W. Miller, M. Boguski, B. Raghavachari, Z. Zhang and R. C. Hardison (1994) Constructing aligned sequence blocks. Journal of Computational Biology 1, 49-61.

robust - from the paper:

K.-M. Chao, R. C. Hardison and W. Miller (1993) Locating well-conserved regions within a pairwise alignment. CABIOS 9, 387-396.

software from the book:

W. Miller. A Software Tools Sampler, Prentice-Hall (1987)

yama - software from the papers:

R. C. Hardison, K.-M. Chao, M. Adamkiewicz, D. Price, J. Jackson, T. Zeigler, N. Stojanovic and W. Miller (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.

R. C. Hardison, K.-M. Chao, S. Schwartz, N. Stojanovic, M. Ganetsky and W. Miller (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.

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

sim96 - submitted to SPEC for use as a benchmark

sim4 - from the paper:

L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998) A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Research 8, 967-974.   ( instructions)

five tools (agree, infocon, phylogen, kkno, kunk) - from the paper:

N. Stojanovic, L. Florea, C. Riemer, D. Gumucio, J. Slightom, M. Goodman, W. Miller, and R. Hardison (1999) Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Research 27, 3899-3910.

support utilities (ntl) - used by the five tools

lat - prints pairwise alignment output as text

laj - interactive tool for viewing and manipulating pairwise alignment output

postprocess - from the paper:

Z. Zhang, P. Berman, T. Wiehe and W. Miller (1999) Post-processing long pairwise alignments. Bioinformatics 15, 1012-1019.

blest - version of sim4 tailored for finding near-identity matches between a genomic sequence and a database of expressed sequences