-
1
-
-
84455200977
-
Modeling large regions in proteins: Applications to loops, termini, and folding
-
Adhikari AN, et al. 2012. Modeling large regions in proteins: applications to loops, termini, and folding. Protein Sci. 21:107-121.
-
(2012)
Protein Sci.
, vol.21
, pp. 107-121
-
-
Adhikari, A.N.1
-
2
-
-
84864446807
-
SeqFIRE: A web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
-
Ajawatanawong P, Atkinson GC, Watson-Haigh NS, Mackenzie B, Baldauf SL. 2012. SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments. Nucleic Acids Res. 40:W340-W347.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W340-W347
-
-
Ajawatanawong, P.1
Atkinson, G.C.2
Watson-Haigh, N.S.3
Mackenzie, B.4
Baldauf, S.L.5
-
3
-
-
0036273056
-
The potential value of indels as phylogenetic markers: Position of trichomonads as a case study
-
Bapteste E, Philippe H. 2002. The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol Biol Evol. 19:972-977.
-
(2002)
Mol Biol Evol.
, vol.19
, pp. 972-977
-
-
Bapteste, E.1
Philippe, H.2
-
4
-
-
74549118866
-
Large-scale parsimony analysis of metazoan indels in protein-coding genes
-
Belinky F, Cohen O, Huchon D. 2010. Large-scale parsimony analysis of metazoan indels in protein-coding genes. Mol Biol Evol. 27:441-451.
-
(2010)
Mol Biol Evol.
, vol.27
, pp. 441-451
-
-
Belinky, F.1
Cohen, O.2
Huchon, D.3
-
5
-
-
84873584506
-
Class of multiple sequence alignment algorithm affects genomic analysis
-
Blackburne BP, Whelan S. 2013. Class of multiple sequence alignment algorithm affects genomic analysis. Mol Biol Evol. 30:642-653.
-
(2013)
Mol Biol Evol.
, vol.30
, pp. 642-653
-
-
Blackburne, B.P.1
Whelan, S.2
-
7
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540-552.
-
(2000)
Mol Biol Evol.
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
8
-
-
33646856440
-
CAFE: A computational tool for the study of gene family evolution
-
De Bie T, Cristianini N, Demuth JP, Hahn MW. 2006. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22:1269-1271.
-
(2006)
Bioinformatics
, vol.22
, pp. 1269-1271
-
-
De Bie, T.1
Cristianini, N.2
Demuth, J.P.3
Hahn, M.W.4
-
10
-
-
84858402388
-
The effects of alignment error and alignment filtering on the sitewise detection of positive selection
-
Jordan G, Goldman N. 2012. The effects of alignment error and alignment filtering on the sitewise detection of positive selection. Mol Biol Evol. 29:1125-1139.
-
(2012)
Mol Biol Evol.
, vol.29
, pp. 1125-1139
-
-
Jordan, G.1
Goldman, N.2
-
11
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh K, Misawa K, Kuma K, Miyata T. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
Miyata, T.4
-
12
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 9:286-298.
-
(2008)
Brief Bioinform.
, vol.9
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
13
-
-
40549095323
-
Local reliability measures from sets of co-optimal multiple sequence alignments
-
Landan G, Graur D. 2008. Local reliability measures from sets of co-optimal multiple sequence alignments. Pac Symp Biocomput. 13:15-24.
-
(2008)
Pac Symp Biocomput.
, vol.13
, pp. 15-24
-
-
Landan, G.1
Graur, D.2
-
14
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin MA, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
-
15
-
-
84910644471
-
Alignment errors strongly impact likelihood-based tests for comparing topologies
-
Levy Karin E, Susko E, Pupko T. 2014. Alignment errors strongly impact likelihood-based tests for comparing topologies. Mol Biol Evol. 31:3057-3067.
-
(2014)
Mol Biol Evol.
, vol.31
, pp. 3057-3067
-
-
Levy Karin, E.1
Susko, E.2
Pupko, T.3
-
16
-
-
80052641540
-
A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes
-
Lin Y, Moret BM. 2011. A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes. J Comput Biol. 18:1055-1064.
-
(2011)
J Comput Biol.
, vol.18
, pp. 1055-1064
-
-
Lin, Y.1
Moret, B.M.2
-
17
-
-
84870822839
-
TIBA: A tool for phylogeny inference from rearrangement data with bootstrap analysis
-
Lin Y, Rajan V, Moret BM. 2012. TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis. Bioinformatics 28:3324-3325.
-
(2012)
Bioinformatics
, vol.28
, pp. 3324-3325
-
-
Lin, Y.1
Rajan, V.2
Moret, B.M.3
-
18
-
-
84993911710
-
Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analyses
-
Lloyd DG, Calder VL. 1991. Multi-residue gaps, a class of molecular characters with exceptional reliability for phylogenetic analyses. J Evol Biol. 4:9-21.
-
(1991)
J Evol Biol.
, vol.4
, pp. 9-21
-
-
Lloyd, D.G.1
Calder, V.L.2
-
19
-
-
46249095233
-
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
-
Loytynoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320:1632-1635.
-
(2008)
Science
, vol.320
, pp. 1632-1635
-
-
Loytynoja, A.1
Goldman, N.2
-
20
-
-
84873193284
-
Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)
-
Luan PT, Ryder OA, Davis H, Zhang YP, Yu L. 2013. Incorporating indels as phylogenetic characters: impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora). Mol Phylogenet Evol. 66:748-756.
-
(2013)
Mol Phylogenet Evol.
, vol.66
, pp. 748-756
-
-
Luan, P.T.1
Ryder, O.A.2
Davis, H.3
Zhang, Y.P.4
Yu, L.5
-
21
-
-
77952304814
-
Alignment of phylogenetically unambiguous indels in Shewanella
-
McCrow JP. 2009. Alignment of phylogenetically unambiguous indels in Shewanella. J Comput Biol. 16:1517-1528.
-
(2009)
J Comput Biol.
, vol.16
, pp. 1517-1528
-
-
McCrow, J.P.1
-
22
-
-
79952386187
-
Human-specific loss of regulatory DNA and the evolution of human-specific traits
-
McLean CY, et al. 2011. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471:216-219.
-
(2011)
Nature
, vol.471
, pp. 216-219
-
-
McLean, C.Y.1
-
23
-
-
70349738209
-
Stochastic models of sequence evolution including insertion-deletion events
-
Miklos I, Novak A, Satija R, Lyngso R, Hein J. 2009. Stochastic models of sequence evolution including insertion-deletion events. Stat Methods Med Res. 18:453-485.
-
(2009)
Stat Methods Med Res.
, vol.18
, pp. 453-485
-
-
Miklos, I.1
Novak, A.2
Satija, R.3
Lyngso, R.4
Hein, J.5
-
24
-
-
84869778772
-
Re-mind the gap! insertion - Deletion data reveal neglected phylogenetic potential of the nuclear ribosomal Internal Transcribed Spacer (ITS) of Fungi
-
Nagy LG, et al. 2012. Re-mind the gap! insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal Internal Transcribed Spacer (ITS) of Fungi. PLoS One 7:e49794.
-
(2012)
PLoS One
, vol.7
, pp. e49794
-
-
Nagy, L.G.1
-
25
-
-
53749107937
-
StatAlign: An extendable software package for joint Bayesian estimation of alignments and evolutionary trees
-
Novak A, Miklos I, Lyngso R, Hein J. 2008. StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics 24:2403-2404.
-
(2008)
Bioinformatics
, vol.24
, pp. 2403-2404
-
-
Novak, A.1
Miklos, I.2
Lyngso, R.3
Hein, J.4
-
26
-
-
33750736013
-
The accuracy of several multiple sequence alignment programs for proteins
-
Nuin PA, Wang Z, Tillier ER. 2006. The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinformatics 7:471.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 471
-
-
Nuin, P.A.1
Wang, Z.2
Tillier, E.R.3
-
27
-
-
84909592569
-
Transfer of noncoding DNA drives regulatory rewiring in bacteria
-
Oren Y, et al. 2014. Transfer of noncoding DNA drives regulatory rewiring in bacteria. Proc Natl Acad Sci U S A. 111:16112-16117.
-
(2014)
Proc Natl Acad Sci U S A.
, vol.111
, pp. 16112-16117
-
-
Oren, Y.1
-
28
-
-
77954270711
-
GUIDANCE: A web server for assessing alignment confidence scores
-
Penn O, Privman E, Ashkenazy H, et al. 2010. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 38:W23-W28.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. W23-W28
-
-
Penn, O.1
Privman, E.2
Ashkenazy, H.3
-
29
-
-
77954288890
-
An alignment confidence score capturing robustness to guide tree uncertainty
-
Penn O, Privman E, Landan G, Graur D, Pupko T. 2010. An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol. 27:1759-1767.
-
(2010)
Mol Biol Evol.
, vol.27
, pp. 1759-1767
-
-
Penn, O.1
Privman, E.2
Landan, G.3
Graur, D.4
Pupko, T.5
-
30
-
-
79953755778
-
A molecular phylogeny of living primates
-
Perelman P, et al. 2011. A molecular phylogeny of living primates. PLoS Genet. 7:e1001342.
-
(2011)
PLoS Genet.
, vol.7
, pp. e1001342
-
-
Perelman, P.1
-
31
-
-
79953716259
-
Resolving difficult phylogenetic questions: Why more sequences are not enough
-
Philippe H, et al. 2011. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 9:e1000602.
-
(2011)
PLoS Biol.
, vol.9
, pp. e1000602
-
-
Philippe, H.1
-
32
-
-
84858383488
-
Improving the performance of positive selection inference by filtering unreliable alignment regions
-
Privman E, Penn O, Pupko T. 2012. Improving the performance of positive selection inference by filtering unreliable alignment regions. Mol Biol Evol. 29:1-5.
-
(2012)
Mol Biol Evol.
, vol.29
, pp. 1-5
-
-
Privman, E.1
Penn, O.2
Pupko, T.3
-
33
-
-
39749111875
-
OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics
-
Ranwez V, et al. 2007. OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. BMC Evol Biol. 7:241.
-
(2007)
BMC Evol Biol.
, vol.7
, pp. 241
-
-
Ranwez, V.1
-
34
-
-
22844450838
-
Joint Bayesian estimation of alignment and phylogeny
-
Redelings BD, Suchard MA. 2005. Joint Bayesian estimation of alignment and phylogeny. Syst Biol. 54:401-418.
-
(2005)
Syst Biol.
, vol.54
, pp. 401-418
-
-
Redelings, B.D.1
Suchard, M.A.2
-
35
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson D, Foulds LR. 1981. Comparison of phylogenetic trees. Math Biosci. 53:131-147.
-
(1981)
Math Biosci.
, vol.53
, pp. 131-147
-
-
Robinson, D.1
Foulds, L.R.2
-
36
-
-
0033793019
-
Rare genomic changes as a tool for phylogenetics
-
Rokas A, Holland PW. 2000. Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol. 15:454-459.
-
(2000)
Trends Ecol Evol.
, vol.15
, pp. 454-459
-
-
Rokas, A.1
Holland, P.W.2
-
37
-
-
70349205853
-
BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC
-
Satija R, Novak A, Miklos I, Lyngso R, Hein J. 2009. BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC. BMC Evol Biol. 9:217.
-
(2009)
BMC Evol Biol.
, vol.9
, pp. 217
-
-
Satija, R.1
Novak, A.2
Miklos, I.3
Lyngso, R.4
Hein, J.5
-
38
-
-
34447280568
-
The relative performance of indel-coding methods in simulations
-
Simmons MP, Muller K, Norton AP. 2007. The relative performance of indel-coding methods in simulations. Mol Phylogenet Evol. 44:724-740.
-
(2007)
Mol Phylogenet Evol.
, vol.44
, pp. 724-740
-
-
Simmons, M.P.1
Muller, K.2
Norton, A.P.3
-
39
-
-
0034350427
-
Gaps as characters in sequence-based phylogenetic analyses
-
Simmons MP, Ochoterena H. 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst Biol. 49:369-381.
-
(2000)
Syst Biol.
, vol.49
, pp. 369-381
-
-
Simmons, M.P.1
Ochoterena, H.2
-
42
-
-
0004248459
-
-
Version 4.0b10. Sunderland MA: Sinauer Associates
-
∗and other methods). Version 4.0b10. Sunderland (MA): Sinauer Associates.
-
(2003)
∗and Other Methods)
-
-
Swofford, D.1
-
43
-
-
34547489084
-
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
-
Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564-577.
-
(2007)
Syst Biol.
, vol.56
, pp. 564-577
-
-
Talavera, G.1
Castresana, J.2
-
44
-
-
1842717956
-
Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes
-
Taylor MS, Ponting CP, Copley RR. 2004. Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. Genome Res. 14:555-566.
-
(2004)
Genome Res.
, vol.14
, pp. 555-566
-
-
Taylor, M.S.1
Ponting, C.P.2
Copley, R.R.3
-
45
-
-
0021084212
-
Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes
-
Templeton AR. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221-244.
-
(1983)
Evolution
, vol.37
, pp. 221-244
-
-
Templeton, A.R.1
-
46
-
-
79953307693
-
A comprehensive benchmark study of multiple sequence alignment methods: Current challenges and future perspectives
-
Thompson JD, Linard B, Lecompte O, Poch O. 2011. A comprehensive benchmark study of multiple sequence alignment methods: current challenges and future perspectives. PLoS One 6:e18093.
-
(2011)
PLoS One
, vol.6
, pp. e18093
-
-
Thompson, J.D.1
Linard, B.2
Lecompte, O.3
Poch, O.4
-
48
-
-
0042697343
-
The evolution of transcriptional regulation in eukaryotes
-
Wray GA, et al. 2003. The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol. 20:1377-1419.
-
(2003)
Mol Biol Evol.
, vol.20
, pp. 1377-1419
-
-
Wray, G.A.1
-
49
-
-
84855824416
-
Accounting for alignment uncertainty in phylogenomics
-
Wu M, Chatterji S, Eisen JA. 2012. Accounting for alignment uncertainty in phylogenomics. PLoS One 7:e30288.
-
(2012)
PLoS One
, vol.7
, pp. e30288
-
-
Wu, M.1
Chatterji, S.2
Eisen, J.A.3
|