87
16. Risso VA, Gavira JA, Gaucher EA et al (2014)
Phenotypic comparisons of consensus variants
versus laboratory resurrections of Precambrian
proteins. Proteins 82:887–896
17. Heinemann U, Hahn M (1995) Circular permutation of polypeptide chains: implications
for protein folding and stability. Prog Biophys
Mol Biol 64:121–143
18. Yang Z, Rannala B (2012) Molecular phylogenetics: principles and practice. Nat Rev Genet
13:303–314
19. Merkl R, Sterner R (2016) Ancestral protein
reconstruction: techniques and applications.
Biol Chem 397:1–21
20. Yang Z (2014) Molecular evolution: a statistical approach. Oxford University Press, Oxford
21. Edgar RC (2004) MUSCLE: multiple
sequence alignment with high accuracy and
high throughput. Nucleic Acids Res 32:
1792–1797
22. Gouy M, Guindon S, Gascuel O (2010)
SeaView version 4: a multiplatform graphical
user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol
27:221–224
23. Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with
variable rates over sites: approximate methods.
J Mol Evol 39:306–314
24. Darriba D, Taboada GL, Doallo R et al (2011)
ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165
25. Guindon S, Dufayard J, Lefort V et al (2010)
New algorithms and methods to estimate
maximum- likelihood phylogenies: assessing
the performance of PhyML 3.0. Syst Biol
59:307–321
26. Yang Z (2007) PAML 4: phylogenetic analysis
by maximum likelihood. Mol Biol Evol
24:1586–1591
27. Kelley LA, Mezulis S, Yates CM et al (2015)
The Phyre2 web portal for protein modeling,
prediction and analysis. Nat Protoc 10:
845–858
28. Okubo Y, Sekiya H, Namiki S et al (2010)
Imaging extrasynaptic glutamate dynamics in
the brain. Proc Natl Acad Sci USA 107:
6526–6531
29. Helmchen F, Denk W (2005) Deep tissue
two- photon microscopy. Nat Methods 2:
932–940
30. Hashimoto H, Isobe K, Suda A et al (2010)
Measurement of two-photon excitation spectra of fluorescent proteins with nonlinear
Fourier- transform spectroscopy. Appl Optics
49:3323–3329
31. Engler C, Kandzia R, Marillonnet S (2008) A
one pot, one step, precision cloning method
with high throughput capability. PLoS One
3:e3647
32. Fu L, Niu B, Zhu Z et al (2012) CD-HIT:
accelerated for clustering the next-generation
sequencing data. Bioinformatics 28:3150–3152
33. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7:
improvements in performance and usability.
Mol Biol Evol 30:772–780
34. Di Tommaso P, Moretti S, Xenarios I et al
(2011) T-Coffee: a web server for the multiple
sequence alignment of protein and RNA
sequences using structural information and
homology extension. Nucleic Acids Res
39:13–17
35. Löytynoja A, Goldman N (2010) webPRANK:
a phylogeny-aware multiple sequence aligner
with interactive alignment browser. BMC
Bioinformatics 11:579
36. Löytynoja A, Goldman N (2008) Phylogenyaware gap placement prevents errors in
sequence alignment and evolutionary analysis.
Science 320:1632–1635
37. Talavera G, Castresana J (2007) Improvement
of phylogenies after removing divergent and
ambiguously aligned blocks from protein
sequence alignments. Syst Biol 56:564–577
38. Nguyen LT, Schmidt HA, Von Haeseler A
et al (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximumlikelihood phylogenies. Mol Biol Evol 32:
268–274
39. Stamatakis A (2014) RAxML version 8: a tool
for phylogenetic analysis and post-analysis
of large phylogenies. Bioinformatics 30:
1312–1313
40. Ashkenazy H, Penn O, Doron-Faigenboim A
et al (2012) FastML: a web server for probabilistic reconstruction of ancestral sequences.
Nucleic Acids Res 40:580–584
41. Lo WC, Wang LF, Liu YY et al (2012) CPred:
a web server for predicting viable circular permutations in proteins. Nucleic Acids Res
40(W1):W232–W237
Improving FRET Sensors by Ancestral Gene Resurrection
16. Risso VA, Gavira JA, Gaucher EA et al (2014)
Phenotypic comparisons of consensus variants
versus laboratory resurrections of Precambrian
proteins. Proteins 82:887–896
17. Heinemann U, Hahn M (1995) Circular permutation of polypeptide chains: implications
for protein folding and stability. Prog Biophys
Mol Biol 64:121–143
18. Yang Z, Rannala B (2012) Molecular phylogenetics: principles and practice. Nat Rev Genet
13:303–314
19. Merkl R, Sterner R (2016) Ancestral protein
reconstruction: techniques and applications.
Biol Chem 397:1–21
20. Yang Z (2014) Molecular evolution: a statistical approach. Oxford University Press, Oxford
21. Edgar RC (2004) MUSCLE: multiple
sequence alignment with high accuracy and
high throughput. Nucleic Acids Res 32:
1792–1797
22. Gouy M, Guindon S, Gascuel O (2010)
SeaView version 4: a multiplatform graphical
user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol
27:221–224
23. Yang Z (1994) Maximum likelihood phylogenetic estimation from DNA sequences with
variable rates over sites: approximate methods.
J Mol Evol 39:306–314
24. Darriba D, Taboada GL, Doallo R et al (2011)
ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27:1164–1165
25. Guindon S, Dufayard J, Lefort V et al (2010)
New algorithms and methods to estimate
maximum- likelihood phylogenies: assessing
the performance of PhyML 3.0. Syst Biol
59:307–321
26. Yang Z (2007) PAML 4: phylogenetic analysis
by maximum likelihood. Mol Biol Evol
24:1586–1591
27. Kelley LA, Mezulis S, Yates CM et al (2015)
The Phyre2 web portal for protein modeling,
prediction and analysis. Nat Protoc 10:
845–858
28. Okubo Y, Sekiya H, Namiki S et al (2010)
Imaging extrasynaptic glutamate dynamics in
the brain. Proc Natl Acad Sci USA 107:
6526–6531
29. Helmchen F, Denk W (2005) Deep tissue
two- photon microscopy. Nat Methods 2:
932–940
30. Hashimoto H, Isobe K, Suda A et al (2010)
Measurement of two-photon excitation spectra of fluorescent proteins with nonlinear
Fourier- transform spectroscopy. Appl Optics
49:3323–3329
31. Engler C, Kandzia R, Marillonnet S (2008) A
one pot, one step, precision cloning method
with high throughput capability. PLoS One
3:e3647
32. Fu L, Niu B, Zhu Z et al (2012) CD-HIT:
accelerated for clustering the next-generation
sequencing data. Bioinformatics 28:3150–3152
33. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7:
improvements in performance and usability.
Mol Biol Evol 30:772–780
34. Di Tommaso P, Moretti S, Xenarios I et al
(2011) T-Coffee: a web server for the multiple
sequence alignment of protein and RNA
sequences using structural information and
homology extension. Nucleic Acids Res
39:13–17
35. Löytynoja A, Goldman N (2010) webPRANK:
a phylogeny-aware multiple sequence aligner
with interactive alignment browser. BMC
Bioinformatics 11:579
36. Löytynoja A, Goldman N (2008) Phylogenyaware gap placement prevents errors in
sequence alignment and evolutionary analysis.
Science 320:1632–1635
37. Talavera G, Castresana J (2007) Improvement
of phylogenies after removing divergent and
ambiguously aligned blocks from protein
sequence alignments. Syst Biol 56:564–577
38. Nguyen LT, Schmidt HA, Von Haeseler A
et al (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximumlikelihood phylogenies. Mol Biol Evol 32:
268–274
39. Stamatakis A (2014) RAxML version 8: a tool
for phylogenetic analysis and post-analysis
of large phylogenies. Bioinformatics 30:
1312–1313
40. Ashkenazy H, Penn O, Doron-Faigenboim A
et al (2012) FastML: a web server for probabilistic reconstruction of ancestral sequences.
Nucleic Acids Res 40:580–584
41. Lo WC, Wang LF, Liu YY et al (2012) CPred:
a web server for predicting viable circular permutations in proteins. Nucleic Acids Res
40(W1):W232–W237
Improving FRET Sensors by Ancestral Gene Resurrection