Classified References on Computational Biology R. C. T. Lee On Books On Classification of Protein Folds On Evolutionary Trees On Divide-and-Conquer

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1

Classified References on Computational Biology

R. C. T. Lee



On Books

On Classification of Protein Folds

On Evolutionary Trees

On Divide
-
and
-
Conquer

On Genome Rearrangement

On LCS

On
Miscellaneous

O
n Nearest Neighbor Search

On Pattern Discovery

On Physical Mapping

On Protein Structure

On RNA Struc
tures

On Sequence Alignment

On Sequence Assembly Problem

On Sorting by Reversal

On String Matchi
ng

On Structure Alignment

On Superstrings

On Superstructures

On Visual Display

On NP
-
Complete Problems and Approximation Algorithms



2

On Sequence Assembly Problem


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L. and Maffioli, F.,
Networks
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[DS1991] A Sequence Assembly and Editing Program for Efficient
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Dean, S. and Staden, R.,

Nucleic Acids Research,
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3917.


[GMSR79] Computer Problems for the Assembly of DNA Sequences,
Gingeras,
T.
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Nucleic Acid Res,

Vol. 7, 1979, pp.
529
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545.


[H92] A Contig Assembly Program Based on Sensitive Detection of Fragments
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Huang, X.,
Genomics,
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-
25.


[HGST86] Efficient algorithm
s for finding minimum spanning trees in
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Combinatorial
, Vol. 6, 1986, pp. 109
-
122.


[KE95] Combinational Algorithms for DNA Sequence Assembly,
Kececioglu, D.
J. and Myers, W
. E.,
Algorithmica,
Vol. 13, 1995, 7
-
51.


[KLT2001
]
A Probabilistic Approach to Sequence Assembly Validation
,
Kim, S.,
Liao, L. and Tomb, J. F.
,

Workshop on Data Mining in Bioinformatics
, 2001


[KM89] A Procedural Interface for a Fragment Assembly Tool,
Kececioglu, D. J.
and Myers, W. E.,

Technical Reports 89
-
5, Department of Computer Science, The
University of Arizona,
1989


[M93] Rethinking the DNA Fragment Assembly Problem,
Meidanis, J., 1993.


[M95]


Towards
S
implifying and
A
ccurately
F
ormulating
F
rag
ment

A
ssembly,

E. W. Myers,

J. Comput. Biology
, Vol. 2, 1995,
pp.
275
-
290


[PTW2001] A New Approach to Fragment Assembly in DNA Sequencing,

Pevzner, P. A., Tang, H. and Waterman, M. S.,
RECOMB, Montreal, Canada,
2001,
pp. 256
-
267.


3







4

On Sequence Alignm
ent


[AAS2000] On Approximation Algorithms for Local Multiple Alignment,
Akutsu, T.
,
Arimura, H.

and Shimozono, S.,

RECOMB, TOKYO,

2000, pp. 1
-
7.



[AKMSW87] Geometric applications of a matrix
-
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209.


[B95] A space efficient algorithm for findin
g the best nonoverlapping
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369.


[BLP97] Approximation Algorithms for Multiple Sequence Alignment
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V., Lawler, E. and Pevzner, P.,
Theoretical Computer Science,
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97, pp.
233
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244.


[BM98] Discovering internet marketing intelligence through online analytical
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SIGMOD Record
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61.


[BV2001] The Complexity of Multiple Sequence Alignment with SP
-
Score

that
is a Metric
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Theoretical Computer Science,
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259, 2001, pp. 63
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79.


[CHM92] Recent Developments in Linear
-
Space Alignment Methods: A Survey,
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J. Comput. Biol.,
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92, pp.
271
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291.



[CL88] The Multiple Sequence Alignment Problem in Biology,
Carrillo,H.

and
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SIAM J. Appl. Math,

Vol. 48, 1988, pp.1073
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1082.



[CL92] Theoretical and Empirical Comparisons of Approximate String
Matching Algorithms,
Chang, W
. I. and Lampe, J.,
In Proceedings of the 3rd
Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer
Science,
Vol. 644, 1992, pp. 172
-
181.



5


[CPM92] Aligning Two Sequences within a Specified Diagonal Band,
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M., Pearson, W. R. and
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Comput. Appl. BioSciences,
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481
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487.


[CWC92] A survey of Multiple Sequence Comparison Methods
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Wong, A. K. C. and Chiu, D. K.Y.
Bull. Math. Biol.

Vol. 54, 1992, pp. 563
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598.


[DH75] Sequence Comparison by Dynami
c Programming ,
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Hansen, P.,

Biometrika,

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664.


[FD87] Progressive Sequence Aligment as a Prerequisite to Correct Phylogenetic
Trees
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J. Molec. Evol.

Vol. 25, 1987, pp. 351
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360.


[FFB2000]

A task
-
based architecture for application
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aware adjuncts
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85.


[G91] Efficient Methods for Multiple Sequence Align
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, Gusfield, D.,
Tech.

Report, Computer Science Division, University
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-
91
-
4
,

1991.


[G93] Efficient Methods for Multiple Sequence Alignment with Guaranteed
Error Bounds
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Bull. Mathemati
cs Biology.
Vol. 55, 1993, pp. 141
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154.


[GBN94] Parametric Optimization of Sequence Alignment
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Balasubramanian, K. and Naor, D.,
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-
5, Oct
-
Nov. 1994,
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[GCS2000] Evaluation Measures of Multiple Sequence
Alignments
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H., Korostensky, C. and Benner,S.,
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-
2, 2000, pp. 261
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276.


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biology
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ci.
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[GMP96] Gene recognition via spliced sequence alignment
, Gelfand, M.,

6

Mironov, A. and Pevzner, P.,
Proc. Natl. Acad. Sci. USA
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9061
-
9066.


[J99] Reducing Gap
-
0 Multiple Alignment to Multiple Alignment
,

Just, W.,
Manuscript
, 1999.


[
K93] The
M
aximun
W
eight
T
race
A
lignment
P
roblem in
M
ultiple
S
equence
A
ligment
, Kececioglu,
J.,

A.
A
postolico, M Crochemore, Z. Galil, U. Manber
(Eds.), Combinatorial Pattern Maching 93, Padova, Italy
, June
,

1993
,

V
ol. 684,
p
p.106
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119.


[KM96] An algorithm for locating non
-
overlapping regions of maximum
alignment score
, Kannan, S. and Myers, E.,
SIAM J. Comput.
, Vol. 25, No. 3, 1996,
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662.


[KRGS2001]
Gene Structure Prediction and Alternative Splicing Analysis
Using G
enomically Aligned ESTs,

Kan,

Z.,
Rouchka,

E. C.,
Gish
,
W
.

R.

and

States,

D. J.,
Genome Research
,
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11
, 2001, pp.
889

900
.


[L88] Computational Molecular Biology, Sources and Methods for Sequence
Analysis,
A. Lesk, ED.,
Oxford University Press,
1988.


[
LAK89]

A
T
ool for
M
ultiple
S
equence
A
ligment
,

Lipman,
D. J.,
Altschul,
S. F.
and
Kececioglu,
J. D.,

Proc. Nat.

Acad Sci.
,

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86
,

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,

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4415.


[LMW99] Finding Similar Regions in Many Sequences
, Li, M., Ma, B. and
Wang, L.,
Proc. 31st ACM Symp
. Theory of Computing (STOC 99) ,
1999.

[LP2000] RNA Pseudoknot Prediction in Energy Based Models,
Lyngso, R. B.
and Pedersen, C. N. S.,
Journal of Computational biology,
Vol.

7,
2000,
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427.


[LPSH2001] Visualization and analysis of clickstream dat
a of online stores for
understanding web merchandising
, Lee, J., Podlaseck, M., Schonberg, E. and Hoch,
R.,
J. Data Mining Knowledge Discovery
, Vol. 5, Nos. 1/2, 2001, pp. 59
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84.


[LR99] Local Multiple Sequence Alignment Using Dead
-
End Elimination,

Lukash
in, A. V. and Rosa, J. J.,
Biogen, Inc, Cambridge Center, USA,
Vol. 15, No.
11, 1999, pp. 947
-
953.



7


[LU2001] On the Common Substring Alignment Problem
, Landau, G. and
Ukelson, M.,
Journal of Algorithms
, Vol. 41, 2001, pp. 338
-
359.


[M88] A Flexible Mult
iple Sequence Alignment Program,
Martinez, M,

Nucleic
Acids Res,

Vol. 16, 1988, pp. 1683
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[MFDW97] DIALIGN: Finding Local Similarities by Multiple Sequence
Alignment,
Morgenstern, B., Frech, K., Dress, A. and Werner, T.,
GSF
-
National
Research Cente
r for Environment and Health,
1997.



[MRPG98] Performance
-
guarantee gene predictions via spliced alignment
,
Mironov, A., Roytberg, M., Pevzner, P. and Gelfand, M.,
Genomics 51 A.N.
GE985251
, 1998, pp. 332
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339.


[MW97]
N
ear

Optimal

Multiple

Alignment

wi
thin a
B
and in
P
olynomial
T
ime,

Ma,

B. and

Wang
,

L
.
,

in the Proc. 32
nd

ACM,
pp. 1
-
23.


[NW70] A General Method Applicable to the Search for Similarities in the
Amino Acid Sequence of Two Proteins
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J.
Mol. Biol.,
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453.



[P92]

Multiple Alignment, Communication Cost, and Graph Matching
, Pevzner,
P. A.,
SIAM Journal on Applied Mathematics,

Vol. 52, No. 6, Dec
.

1992, pp.
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Sellers, P. H.,
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154.



[S2001] Non
-
Approximability of Weighted Multiple Sequence Alignment,

Siebert, B.,
COCOON,
2001, PP. 75
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85.


[SBDGGHHLKMPS91] A system for distributed intrusion detection
, Snapp, S
.,
Brentano, J., Dias, G., Goan, T., Grance, T., Heberlein, L., Ho, C., Levitt, K.,
Mukerjee, B., Mansur, D., Pon, K. and Smaha, S.,
COMPCON Spring 91, the 36
th

IEEE International Computer Conference
, 1991, pp. 170
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176.



8

[SM86] A Multiple Sequence Aligmen
t Program,
Sobel, E. And Martinez, M.,

Nucleic Acids Res.,
Vol. 14, 1986, pp. 363
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374.


[SP97] Las Vegas algorithms for gene recognition: Suboptimal and
error
-
tolerant spliced alignment
, Sze, S. and Pevzner,
P., J. Comp. Biol.
, Vol. 4, No.
3, 1997, pp. 29
7
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309.


[
SYYH02] Super Pairwise Alignment (SPA): An Efficient Approach to Global
Alignment for Homologous Sequence, Shen
, S. Y., Yang, J., Yao, A., and Hwang, P.
I.,
Journal of Computational Biology
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486.


[SZ90] Fast Algorithm for t
he Unit Cost Editing Distance between Trees
,
Shasha, D. and Zhang, K.,
J. Algorithms
, Vol. 11, 1990, pp. 581
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621.


[
T90]

Hierarchical
M
ethod to
A
lign
L
arge
N
umbers of

B
iological
S
equences
,

Taylor,

W. R.,

Mothods Enzymol.

Vol.
183
,

1990
, pp.

456
-
474.


[UHL
U] Using repeats to speedup DNA sequence alignment, private
communication
, Ukelson, M., Horesh, Y., Landau, G. and Unger, R.


[
VLP94]


Approximation
A
lgorithms for Multiple Sequence Alignment
, Bafna,

V.,
Lawler,

E. L. and

Pevzner,
P.,
Proc.


of the 5th
A
n
nual Symp. on Combin. Pattern
M
a
t
ching(CPM'94). Lecture Notes in Computer Science
,
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ol.

807, 1974, pp.
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53.


[WJ94]
On the
C
omplexity of
M
ultiple
S
equence
A
lignment
,
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T.
,
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,

Vol. 1, 1994, pp.

337
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[W9
5] A Simplified Proof of the NP
-

and MAX SNP
-
Hardness of Multiple
Sequence Tree Alignments,

Wareham, H. T.,
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[WJ94] On the Complexity of Multiple Sequence Aligment ,
Wang, L. and Jiang,
T.,
J. Comput.

Biol.,

Vol. 1, 1994, pp. 337
-
348.



[
WSB76]

S
ome
B
iological
S
equence
M
etrics
,
Waterman,
M. S.,

Smith,

T. F. and

Beyer,
W. A.,
Adv. In Math.

Vol.
20
,
1976
,

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367
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9

[Z96] A Constrained Edit Distance between Unordered Labeled Trees
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K.,
Alg
orithmica
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[ZSS92] On the Editing Distance between unordered Labeled Trees
, Zhang, K.,
Statman, R. and Shasha, D.,
Information Processing Letters
, Vol. 42, 1992, pp.
133
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139.



10

On Evolutionary Trees


[AG83]
Human Mitochondri
al DNA Variation and Evolution: Analysis of
Nucleotide Sequences from Seven Individuals
,
Aquadro, C. F. and Greenberg, B. D.,

Genetics,

Vol. 103, 1983, pp. 287
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312.


[AK97] Maximun Agreement Subtree in a Set of Evolutionary Trees: Metrics
and Efficient Al
gorithms,
Amir, A and Keselman, D.,
SIAM J. Comput.,
Vol. 26,
1997, pp. 1656
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1669.


[B71] The Recovery of Trees from Measures of Dissimilarity,

Buneman, P.,

Mathematics in the Archaeological and Historical Sciences,
1971 , pp. 387
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395.


[BBJKLWZ2000] P
ractical Algorithm for Recovering the Best Supported
Edges in an Evolutionary Tree
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Wareham, T., and Zhang, H.,
Proc. 11th Annual ACM
-
SIAM Symp. on Discrete

Algorithms,
Jan. 2000.


[BPWW82]
Mitochond
rial DNA Sequences of Primates: Tempo and Mode of
Evolution,

Brown, W. M., Prager, E. M., Wang, A. and Wilson, A. C.,

Journal of
Molecular Evolution,

Vol.18,
1982,
pp.225
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239.


[BSLGDV98] The Discovery of Two New Divergent STLVs has Implications for
the E
volution and Epidemiology of HTLVs,
Brussel, M. V., Salemi, M., Liu, H. F.,
Goubau, P., Desmyter, J. and Vandamme, A. M.,
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[CBW84]
Polymorphic Sites and the Mechanism of Evolution in Human
Mitochondrial DNA
,
Ca
nn, R. L., Brown, W. M.

and

Wilson, A. C.,
Genetics,

Vol.
106,

,

1984
,
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[CR89] A Fast Algorithm for Constructing Trees from Distance Matrices,
Culbertson, J. C. and Rudnicki, P.,
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215
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220.


[C
SW87]
Mitochondrial DNA and Human Evolution,
Cann, R. L., Stoneking, M.

and

Wilson, A. C.,
Nature,

Vol. 325, 1987, pp. 31
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36.



11

[F81] Evolutionary Trees from DNA sequences: A Maximum Likelihood
Approach,
Felsenstein, J.,
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981.



[F88] Phylogenies from Molecular Sequences: Inference and Reliability,

Felsenstein, J.,
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Vol. 22, 1988, pp. 521
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[FKW95]

A Robust Model for Finding Optimal Evolutionary Trees
, Farach, M.,
Kannan, S. and Warnow, T.,
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ca
, Vol. 13, No. 1
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2, Jan
-
Feb. 1995, pp.
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[FM67]

Construction of Phylogenetic Trees
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Science
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[FT97] Sparse Dynamic Programming for Evolutionary Tree Comparison
,
Farach, M
. and Thorup, M.,

SIAM J. Comput.
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230.


[HH90] Intraspecific Nucleotide Sequence Differences in the Major Noncoding
Region of Human Mitochondrial DNA,

Horai
,

S. and Hayasaka,
Am. J. Hum
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.


[HH91] Time

of the Deepest Root for Polymorphism in Human Mitochondrial
DNA,
Hasegawa, M. and Horai, S.,
Journal of Molecular Evolution
,

Vol. 32, 1991,
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[HT84] Fast Algorithms for Finding Nearest Common Ancestors,

D. Harel and R.
E. Tarjan,
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V
ol. 13, No.2, 1984, pp.338
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355.


[JKL2001] A Polynomial Time Approximation Scheme For Inferring
Evolutionary Trees From Quartet Topologies and Its Application,
Jiang, T.,
Kearney, P. and Li, M.,
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[JLW94
]

Aligning Sequences via an Evolutionary Tree
, Jiang, T., Lawler, E. L.
and Wang, L.
,

Conference Proceedings of the Annual ACM Symposium on
Theory of Computing
, May 23
-
25, 1994, pp.

760
-
769.


[KG98] Reconstructing a History of Recombination from a Set of

Sequences
,
Kececioglu, J. and Gusfield, D.,
Discrete Applied Mathematics
, Vol. 88, 1998, pp.
239
-
260.


12


[KHM97] Inferring Evolutionary Trees from Ordinal Data
, Kearney, P.,
Hayward, R. B. and Meijer, H.
Proc. 8th Annual ACM
-
SIAM Symposium on
Discrete Algo
rithms,

1997, pp. 418
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[KLW96] Determining the Evolutionary Tree Using Experiments,
Kannan, S. K.,
Lawler, E. L. and Warnow, T. J.,
J. Algorithms,
Vol. 21, 1996, pp. 26
-
50.


[KW94]

Inferring Evolutionary History from DNA Sequences,
Kannan, S. K.
a
nd Warnow, T. J.
,

SIAM Journal on Computing
, Vol. 23, No. 4, Aug. 1994, pp.
713
-
737.


[KW95] Tree Reconstruction from Partial Orders
, Kannan, S. and Warnow; T.,
SIAM J. Computing
, Vol. 24, 1995, pp. 511
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519.


[KWY98] Computing the Local Consensus of Tre
es
, Kannan, S., Warnow, T. and
Yooseph, S.,
SIAM Journal on Computing
, Vol. 27, No. 6, Dec. 1998,
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1724.


[LBC96] An Evolutionary Trace Method Defines Binding Surfaces Common to
Protein Families,
Lichtarge, O., Bourne, H. R. and Cohen, F. E.,
Journ
al Comput.
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358.


[LCJDLG98] Molecular Analysis of GB Virus C Isolates in Belgian
Hemodialysis Patients,
Liu, H. F., Cornu, C., Jadoul, M., Dahan, K., Loute, G. and
Goubau, P.,
Journal of Medical Virology,
Vol. 55, 1998, pp.

118
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[LMTDDG2000] High Prevalence of GB Virus C/Hepatities G Virus in
Kinshasa, Democratic Republic of Congo: A Phylogenetic Analysis,
Liu, H. F.,
Muyembe
-
Tamfum, J. J., Dahan K., Desmyter, J. and Goubau, P.,
Journal of Medical
Virology,
Vol. 60,
2000, pp. 159
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[S75]

Minimum
M
utation
T
ree of
S
equences
,

Sankoff,
D.
,

SIAM J. Appl.

Math.,

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28
,
1975
, pp.
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Origin of Early Modern Humans,

Stringer,

C. B.,
ibid,
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244.



13

[S92] The Complexity of Reconstructing Trees fro
m Qualitative Characters
and Subtrees
, Steel, M.,
Journal of Classification
, Vol. 9, 1992 , pp. 91
-
116.


[SA83] Phylogeny and Classification of Birds Based on the Data of
DNA
-
DNA
-
Hybridization,
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1
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C. B. and Andrews, P.,
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1268.


[SH96] Quartet Puzzling : A Quartet Maximum
-
Likelihood Method for
Reconstructing Tree Topolog
ies,
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Molecular
Biology and Evolution,
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969.


[SJBW90] Geographic Variation in Human Mitochondrial DNA from Papua
New Guinea,
Stoneking, M., Jorde, L. B., Bhatia, K.

and

Wilson, A. C.,
Genetics,
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124, 1990, pp.717
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733.


[SN87] The Neighbor
-
Joining Method : A New Method for Reconstructing
Phylogenetic Trees,
Staitou, N. and Nei, M.,
Molecular Biology and Evolution,
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4, 1987, pp. 406
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425.



[SV88] On Finding Lowest Common Ancestors: Simplificati
on and
Parallelization,

B. Schieber and U. Vishkin.,
SIAM J. Comput.,

Vol. 17, 1988,
pp.1253
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1262.


[T91] Human Origins and Analysis of Mitochondrial DNA Sequences,
Templeton, A.,
Science,
Vol. 255, 1991, pp. 737.


[VPHKW89]
Mitochondrial DNA Sequences i
n Single Hairs from a Southern
African Population
,
Vigilant, R., Pennington, Harpending, H., Kocher, T. D.

and

Wilson, A. C.
, Proc. Natl. Acad. U.S.A.
, Vol. 86, 1989, pp. 9350
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9354.


[VSHHW91]

African Populations and the Evolution of Human Mitochondrial
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23

On String Matching


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On Superstructures


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43

On Books


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On Sorting by Reversal


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47

On Visual
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