-
1
-
-
0034712743
-
The new animal phylogeny: reliability and implications
-
Adoutte A., Balavoine N., Lartillot G., Lespinet B., Prud'homme O., and de Rosa R. The new animal phylogeny: reliability and implications. Proc. Natl Acad. Sci. USA 97 (2000) 4453-4456
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 4453-4456
-
-
Adoutte, A.1
Balavoine, N.2
Lartillot, G.3
Lespinet, B.4
Prud'homme, O.5
de Rosa, R.6
-
2
-
-
10044294457
-
Common intervals and sorting by reversals: a marriage of necessity
-
Bergeron A., Heber S., and Stoye J. Common intervals and sorting by reversals: a marriage of necessity. Bioinformatics 18 (2002) S54-S63
-
(2002)
Bioinformatics
, vol.18
-
-
Bergeron, A.1
Heber, S.2
Stoye, J.3
-
3
-
-
0032770572
-
Gene order breakpoint evidence in animal mitochondrial phylogeny
-
Blanchette M., Kunisawa T., and Sankoff D. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49 (1999) 193-203
-
(1999)
J. Mol. Evol.
, vol.49
, pp. 193-203
-
-
Blanchette, M.1
Kunisawa, T.2
Sankoff, D.3
-
4
-
-
0033561361
-
Animal mitochondrial genomes
-
Boore J.L. Animal mitochondrial genomes. Nucl. Acids Res. 27 (1999) 1767-1780
-
(1999)
Nucl. Acids Res.
, vol.27
, pp. 1767-1780
-
-
Boore, J.L.1
-
5
-
-
0031769998
-
Big trees from little genomes: mitochondrial gene order as a phylogenetic tool
-
Boore J.L., and Brown W.M. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Curr. Opinion Gen. Dev. 8 (1998) 668-674
-
(1998)
Curr. Opinion Gen. Dev.
, vol.8
, pp. 668-674
-
-
Boore, J.L.1
Brown, W.M.2
-
6
-
-
0036143403
-
Genome-scale evolution: reconstructing gene orders in ancestral species
-
Bourque G., and Pevzner P.A. Genome-scale evolution: reconstructing gene orders in ancestral species. Genome Res. 12 (2002) 26-36
-
(2002)
Genome Res.
, vol.12
, pp. 26-36
-
-
Bourque, G.1
Pevzner, P.A.2
-
7
-
-
0027840782
-
Applications of approximate string matching to 2D shape recognition
-
Bunke H., and Bühler U. Applications of approximate string matching to 2D shape recognition. Pattern Recognition. 26 (1993) 1797-1812
-
(1993)
Pattern Recognition.
, vol.26
, pp. 1797-1812
-
-
Bunke, H.1
Bühler, U.2
-
8
-
-
0037417915
-
Unique mitochondrial genome architecture in unicellular relatives of animals
-
Burger G., Forget L., Zhu Y., Gray M.W., and Lang F.B. Unique mitochondrial genome architecture in unicellular relatives of animals. Proc. Natl Acad. Sci. USA 100 (2003) 892-897
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 892-897
-
-
Burger, G.1
Forget, L.2
Zhu, Y.3
Gray, M.W.4
Lang, F.B.5
-
9
-
-
0346882654
-
Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case
-
Coenye T., and Vandamme P. Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case. Microbiology 149 (2003) 3507-3517
-
(2003)
Microbiology
, vol.149
, pp. 3507-3517
-
-
Coenye, T.1
Vandamme, P.2
-
10
-
-
0034918386
-
A sequence alignment algorithm with an arbitrary gap penalty function
-
Dewey T.G. A sequence alignment algorithm with an arbitrary gap penalty function. J. Comput. Biol. 8 (2001) 177-190
-
(2001)
J. Comput. Biol.
, vol.8
, pp. 177-190
-
-
Dewey, T.G.1
-
11
-
-
0026781151
-
Chloroplast DNA inversions and the origin of the grass family (poaceae)
-
Doyle J.J., Davis J.I., Soreng R.J., Garvin D., and Anderson M.J. Chloroplast DNA inversions and the origin of the grass family (poaceae). Proc. Natl Acad. Sci. USA 89 (1992) 7722-7726
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 7722-7726
-
-
Doyle, J.J.1
Davis, J.I.2
Soreng, R.J.3
Garvin, D.4
Anderson, M.J.5
-
12
-
-
1942485834
-
The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca)
-
Dreyer H., and Steiner G. The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca). Mol. Phylogenet. Evol. 31 (2004) 605-617
-
(2004)
Mol. Phylogenet. Evol.
, vol.31
, pp. 605-617
-
-
Dreyer, H.1
Steiner, G.2
-
13
-
-
0242318326
-
Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes
-
Faith J.J., and Pollock D.D. Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics 165 (2003) 735-745
-
(2003)
Genetics
, vol.165
, pp. 735-745
-
-
Faith, J.J.1
Pollock, D.D.2
-
14
-
-
0000122573
-
Phylip-phylogeny inference package (version 3.2)
-
Felsenstein J. Phylip-phylogeny inference package (version 3.2). Cladistics 5 (1989) 164-166
-
(1989)
Cladistics
, vol.5
, pp. 164-166
-
-
Felsenstein, J.1
-
15
-
-
0033231209
-
Whole genome-based phylogenetic analysis of free-living microorganisms
-
Fitz-Gibbon S.T., and House C.H. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucl. Acids Res. 27 (1999) 4218-4222
-
(1999)
Nucl. Acids Res.
, vol.27
, pp. 4218-4222
-
-
Fitz-Gibbon, S.T.1
House, C.H.2
-
16
-
-
1842690043
-
The footprint sorting problem
-
Fried C., Hordijk W., Prohaska S.J., Stadler C.R., and Stadler P.F. The footprint sorting problem. J. Chem. Inf. Comput. Sci. 44 (2004) 332-338
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 332-338
-
-
Fried, C.1
Hordijk, W.2
Prohaska, S.J.3
Stadler, C.R.4
Stadler, P.F.5
-
17
-
-
0020484488
-
An improved algorithm for matching biological sequences
-
Gotoh O. An improved algorithm for matching biological sequences. J. Mol. Biol. 162 (1982) 705-708
-
(1982)
J. Mol. Biol.
, vol.162
, pp. 705-708
-
-
Gotoh, O.1
-
18
-
-
0027539635
-
Dynamic programming alignment of sequences representing cyclic patterns
-
Gregor J., and Thomason M.G. Dynamic programming alignment of sequences representing cyclic patterns. IEEE Trans. Patt. Anal. Mach. Intell. 15 (1993) 129-135
-
(1993)
IEEE Trans. Patt. Anal. Mach. Intell.
, vol.15
, pp. 129-135
-
-
Gregor, J.1
Thomason, M.G.2
-
19
-
-
0002856077
-
Turning cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals
-
Hannenhalli S., and Pevzner P.A. Turning cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACM 46 (1999) 1-27
-
(1999)
J. ACM
, vol.46
, pp. 1-27
-
-
Hannenhalli, S.1
Pevzner, P.A.2
-
20
-
-
0028806782
-
Genome sequence comparison and scenarios for gene rearrangements: a test case
-
Hannenhalli S., Chappey C., Koonin E.V., and Pevzner P.A. Genome sequence comparison and scenarios for gene rearrangements: a test case. Genomics 30 (1995) 299-311
-
(1995)
Genomics
, vol.30
, pp. 299-311
-
-
Hannenhalli, S.1
Chappey, C.2
Koonin, E.V.3
Pevzner, P.A.4
-
21
-
-
0142075820
-
The evolution of tRNA-Leu genes in animal mitochondrial genomes
-
Higgs P.G., Jameson D., Jow H., and Rattray M. The evolution of tRNA-Leu genes in animal mitochondrial genomes. J. Mol. Evol. 57 (2003) 435-445
-
(2003)
J. Mol. Evol.
, vol.57
, pp. 435-445
-
-
Higgs, P.G.1
Jameson, D.2
Jow, H.3
Rattray, M.4
-
22
-
-
0026740213
-
A novel mitochondrial genome organization for the blue mussel, Mytilus edulis
-
Hoffmann R.J., Boore J.L., and Brown W.M. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131 (1992) 397-412
-
(1992)
Genetics
, vol.131
, pp. 397-412
-
-
Hoffmann, R.J.1
Boore, J.L.2
Brown, W.M.3
-
23
-
-
0037248815
-
OGRe: a relational database for comparative analysis of mitochondrial genomes
-
Jameson D., Gibson A.P., Hudelot C., and Higgs P.G. OGRe: a relational database for comparative analysis of mitochondrial genomes. Nucl. Acids Res. 31 (2003) 202-206
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 202-206
-
-
Jameson, D.1
Gibson, A.P.2
Hudelot, C.3
Higgs, P.G.4
-
24
-
-
11144329138
-
Mitochondrial genome of the komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements
-
Kumazawa Y., and Endo H. Mitochondrial genome of the komodo dragon: efficient sequencing method with reptile-oriented primers and novel gene rearrangements. DNA Res. 11 (2004) 115-125
-
(2004)
DNA Res.
, vol.11
, pp. 115-125
-
-
Kumazawa, Y.1
Endo, H.2
-
25
-
-
33644881802
-
A gene order database of plastid genomes
-
Kurihara K., and Kunisawa T. A gene order database of plastid genomes. Data Sci. J. 3 (2004) 60-79
-
(2004)
Data Sci. J.
, vol.3
, pp. 60-79
-
-
Kurihara, K.1
Kunisawa, T.2
-
27
-
-
0036434711
-
Bayesian phylogenetic inference from animal mitochondrial genome arrangements
-
Larget B., and Simon D.L. Bayesian phylogenetic inference from animal mitochondrial genome arrangements. J. Royal Statist. Soc. B 64 (2002) 681-693
-
(2002)
J. Royal Statist. Soc. B
, vol.64
, pp. 681-693
-
-
Larget, B.1
Simon, D.L.2
-
28
-
-
0036146407
-
Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss
-
Lavrov D.V., Boore J.L., and Brown W.M. Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. Mol. Biol. Evol. 19 (2002) 163-169
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 163-169
-
-
Lavrov, D.V.1
Boore, J.L.2
Brown, W.M.3
-
29
-
-
0035102453
-
An information based sequence distance and its application to whole mitochondrial genome phylogeny
-
Li M., Badger J.H., Chen X., Kwong S., Kearney P., and Zhang H. An information based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 17 (2001) 149-154
-
(2001)
Bioinformatics
, vol.17
, pp. 149-154
-
-
Li, M.1
Badger, J.H.2
Chen, X.3
Kwong, S.4
Kearney, P.5
Zhang, H.6
-
30
-
-
10644294829
-
The similarity metric
-
Li M., Chen X., Li X., Ma B., and Vitanyi P. The similarity metric. IEEE Trans. Inf. Theory 50 (2004) 3250-3264
-
(2004)
IEEE Trans. Inf. Theory
, vol.50
, pp. 3250-3264
-
-
Li, M.1
Chen, X.2
Li, X.3
Ma, B.4
Vitanyi, P.5
-
31
-
-
0031984285
-
Tandem duplication via light-strand synthesis may provide a precursor for mitochondrial genomic rearrangement
-
Macey J.R., Schulte II J.A., Larson A., and Papenfuss T.J. Tandem duplication via light-strand synthesis may provide a precursor for mitochondrial genomic rearrangement. Mol. Biol. Evol. 15 (1998) 71-75
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 71-75
-
-
Macey, J.R.1
Schulte II, J.A.2
Larson, A.3
Papenfuss, T.J.4
-
32
-
-
4344579582
-
Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences
-
Macey J.R., Papenfuss T.J., Kuehl J.V., Fourcade H.M., and Boore J.L. Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences. Mol. Phylogenet. Evol. 33 (2004) 22-31
-
(2004)
Mol. Phylogenet. Evol.
, vol.33
, pp. 22-31
-
-
Macey, J.R.1
Papenfuss, T.J.2
Kuehl, J.V.3
Fourcade, H.M.4
Boore, J.L.5
-
33
-
-
0025437146
-
On a cyclic string-to-string correction problem
-
Maes M. On a cyclic string-to-string correction problem. Inf. Process. Lett. 35 (1990) 73-78
-
(1990)
Inf. Process. Lett.
, vol.35
, pp. 73-78
-
-
Maes, M.1
-
34
-
-
0032169857
-
Multiple independent origins of mitochondrial gene order in birds
-
Mindell D.P., Sorenson M.D., and Dimcheff D.E. Multiple independent origins of mitochondrial gene order in birds. Proc. Natl Acad. Sci. USA 95 (1998) 10693-10697
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 10693-10697
-
-
Mindell, D.P.1
Sorenson, M.D.2
Dimcheff, D.E.3
-
36
-
-
23844520968
-
Steps toward accurate reconstructions of phylogenies from gene-order data
-
Moret B.M.E., Tang J., Wang L.-S., and Warnow T. Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65 (2002) 508-525
-
(2002)
J. Comput. Syst. Sci.
, vol.65
, pp. 508-525
-
-
Moret, B.M.E.1
Tang, J.2
Wang, L.-S.3
Warnow, T.4
-
37
-
-
0037459349
-
Hexapod origins: monophyletic or paraphyletic?
-
Nardi F., Spinsanti G., Boore J.L., Carapelli A., Dallai R., and Frati F. Hexapod origins: monophyletic or paraphyletic?. Science 299 (2003) 1887-1889
-
(2003)
Science
, vol.299
, pp. 1887-1889
-
-
Nardi, F.1
Spinsanti, G.2
Boore, J.L.3
Carapelli, A.4
Dallai, R.5
Frati, F.6
-
38
-
-
1642578795
-
Plastid genomes of higher plants and algae: structure and functions
-
Translated from Molekulyarnaya Biologiya, 2003, 37(5), 768-783
-
Odintsova M.S., and Yurina N.P. Plastid genomes of higher plants and algae: structure and functions. Mol. Biol. (Mosk.) 37 (2003) 649-662 Translated from Molekulyarnaya Biologiya, 2003, 37(5), 768-783
-
(2003)
Mol. Biol. (Mosk.)
, vol.37
, pp. 649-662
-
-
Odintsova, M.S.1
Yurina, N.P.2
-
39
-
-
0442292205
-
Complete mitochondrial dna sequence of the sea-firefly, Vargula hilgendorfii (crustacea, ostracoda) with duplicate control regions
-
Ogoh K., and Ohmiya Y. Complete mitochondrial dna sequence of the sea-firefly, Vargula hilgendorfii (crustacea, ostracoda) with duplicate control regions. Gene 327 (2004) 131-139
-
(2004)
Gene
, vol.327
, pp. 131-139
-
-
Ogoh, K.1
Ohmiya, Y.2
-
40
-
-
1242335920
-
Whole proteome prokaryote phylogeny without sequence alignment: a k-string composition approach
-
Qi J., Wang B., and Hao B.-l. Whole proteome prokaryote phylogeny without sequence alignment: a k-string composition approach. J. Mol. Evol. 58 (2004) 1-11
-
(2004)
J. Mol. Evol.
, vol.58
, pp. 1-11
-
-
Qi, J.1
Wang, B.2
Hao, B.-l.3
-
41
-
-
0035845536
-
Incomplete taxon sampling is not a problem for phylogenetic inference
-
Rosenberg M.S., and Kumar S. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl Acad. Sci. USA 11 (2001) 10751-10756
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.11
, pp. 10751-10756
-
-
Rosenberg, M.S.1
Kumar, S.2
-
42
-
-
0023375195
-
The neighbor-joining method: a new method for reconstructing phylogenetic trees
-
Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 (1987) 406-425
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
43
-
-
0031721577
-
Multiple genome rearrangement and breakpoint phylogeny
-
Sankoff D., and Blanchette M. Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol. 5 (1998) 555-560
-
(1998)
J. Comput. Biol.
, vol.5
, pp. 555-560
-
-
Sankoff, D.1
Blanchette, M.2
-
44
-
-
0032700064
-
Phylogenetic invariants for genome rearrangements
-
Sankoff D., and Blanchette M. Phylogenetic invariants for genome rearrangements. J. Comput. Biol. 6 (1999) 431-435
-
(1999)
J. Comput. Biol.
, vol.6
, pp. 431-435
-
-
Sankoff, D.1
Blanchette, M.2
-
45
-
-
0026680446
-
Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome
-
Sankoff D., Leduc G., Antoine N., Paquin B., Lang B.F., and Cedergren R. Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc. Natl Acad. Sci. USA 89 (1992) 6575-6579
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 6575-6579
-
-
Sankoff, D.1
Leduc, G.2
Antoine, N.3
Paquin, B.4
Lang, B.F.5
Cedergren, R.6
-
46
-
-
0032900532
-
Genome phylogeny based on gene content
-
Snel B., Bork P., and Huynen M.A. Genome phylogeny based on gene content. Nature Genet. 21 (1999) 108-110
-
(1999)
Nature Genet.
, vol.21
, pp. 108-110
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
47
-
-
0000825481
-
A statistical method for evaluating systematic relationships
-
Sokal R.R., and Michener C.D. A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull. 38 (1958) 1409-1438
-
(1958)
Univ. Kansas Sci. Bull.
, vol.38
, pp. 1409-1438
-
-
Sokal, R.R.1
Michener, C.D.2
-
48
-
-
0033595767
-
Analysis of the complete mitochondrial dna sequence of the brachiopod Terebratulina retusa places brachiopoda within the protostomes
-
Stechmann A., and Schlegel M. Analysis of the complete mitochondrial dna sequence of the brachiopod Terebratulina retusa places brachiopoda within the protostomes. Proc. R. Soc. Lond. B 266 (1999) 1-10
-
(1999)
Proc. R. Soc. Lond. B
, vol.266
, pp. 1-10
-
-
Stechmann, A.1
Schlegel, M.2
-
49
-
-
17044408705
-
Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements
-
Sun H., Zhou K., and Song D. Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements. Gene 349 (2005) 207-217
-
(2005)
Gene
, vol.349
, pp. 207-217
-
-
Sun, H.1
Zhou, K.2
Song, D.3
-
50
-
-
33646795500
-
-
Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.0b10 (Handbook and Software) Sinauer Associates, Sunderland, MA.
-
-
-
-
51
-
-
0001140522
-
Phylogeny reconstruction
-
Hillis D.M., and Moritz C. (Eds), Sinauer Associates, Sunderland, MA
-
Swofford D.L., and Olsen G.J. Phylogeny reconstruction. In: Hillis D.M., and Moritz C. (Eds). Molecular Systematics (1990), Sinauer Associates, Sunderland, MA 411-501
-
(1990)
Molecular Systematics
, pp. 411-501
-
-
Swofford, D.L.1
Olsen, G.J.2
-
52
-
-
0027968068
-
CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice
-
Thompson J.D., Higgs D.G., and Gibson T.J. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice. Nucl. Acids Res. 22 (1994) 4673-4680
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgs, D.G.2
Gibson, T.J.3
-
53
-
-
0036398086
-
Molecular phylogenetics and mitochondrial genomic evolution in the chamaeleonidae (reptilia, squamata)
-
Townsend T., and Larson A. Molecular phylogenetics and mitochondrial genomic evolution in the chamaeleonidae (reptilia, squamata). Mol. Phylogenet. Evol. 23 (2002) 22-36
-
(2002)
Mol. Phylogenet. Evol.
, vol.23
, pp. 22-36
-
-
Townsend, T.1
Larson, A.2
-
55
-
-
21144458976
-
The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (lycopodiaceae)
-
Wolf P.G., Karol K.G., Mandoli D.F., Kuehl J., Arumuganathan K., Ellis M.W., Mishler B.D., Kelch D.G., Olmstead R.G., and Boore O. The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (lycopodiaceae). Gene 350 (2005) 117-128
-
(2005)
Gene
, vol.350
, pp. 117-128
-
-
Wolf, P.G.1
Karol, K.G.2
Mandoli, D.F.3
Kuehl, J.4
Arumuganathan, K.5
Ellis, M.W.6
Mishler, B.D.7
Kelch, D.G.8
Olmstead, R.G.9
Boore, O.10
-
56
-
-
0037633395
-
Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (crustacea: Decapoda: Brachyura)
-
Yamauchi M.M., Miya M.U., and Nishida M. Complete mitochondrial DNA sequence of the swimming crab, Portunus trituberculatus (crustacea: Decapoda: Brachyura). Gene 311 (2003) 129-135
-
(2003)
Gene
, vol.311
, pp. 129-135
-
-
Yamauchi, M.M.1
Miya, M.U.2
Nishida, M.3
|