-
1
-
-
36049030256
-
Mitogenomic analyses of caniform relationships
-
Arnason U., Gullberg A., Janke A., Kullberg M. Mitogenomic analyses of caniform relationships. Mol. Phylogenet. Evol. 2007, 45:863-874.
-
(2007)
Mol. Phylogenet. Evol.
, vol.45
, pp. 863-874
-
-
Arnason, U.1
Gullberg, A.2
Janke, A.3
Kullberg, M.4
-
2
-
-
84865475040
-
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
-
Baele G., Lemey P., Bedford T., Rambaut A., Suchard M.A., Alekseyenko A.V. Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol. 2012, 29:2157-2167.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 2157-2167
-
-
Baele, G.1
Lemey, P.2
Bedford, T.3
Rambaut, A.4
Suchard, M.A.5
Alekseyenko, A.V.6
-
3
-
-
33846799228
-
Variation in evolutionary processes at different codon positions
-
Bofkin L., Goldman N. Variation in evolutionary processes at different codon positions. Mol. Biol. Evol. 2007, 24:513-521.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 513-521
-
-
Bofkin, L.1
Goldman, N.2
-
4
-
-
9944255059
-
Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards
-
Brandley M.C., Schmitz A., Reeder T.W. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 2005, 54:373-390.
-
(2005)
Syst. Biol.
, vol.54
, pp. 373-390
-
-
Brandley, M.C.1
Schmitz, A.2
Reeder, T.W.3
-
5
-
-
37249003697
-
The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics
-
Brown J.M., Lemmon A.R. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst. Biol. 2007, 56:643-655.
-
(2007)
Syst. Biol.
, vol.56
, pp. 643-655
-
-
Brown, J.M.1
Lemmon, A.R.2
-
7
-
-
84864530626
-
Bayesian phylogenetics with BEAUti and the BEAST 1.7
-
Drummond A.J., Suchard M.A., Xie D., Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29:1969-1973.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1969-1973
-
-
Drummond, A.J.1
Suchard, M.A.2
Xie, D.3
Rambaut, A.4
-
8
-
-
84858778486
-
Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation
-
Duchêne S., Archer F.I., Vilstrup J., Caballero S., Morin P.A. Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation. PLoS One 2011, 6:e27138.
-
(2011)
PLoS One
, vol.6
-
-
Duchêne, S.1
Archer, F.I.2
Vilstrup, J.3
Caballero, S.4
Morin, P.A.5
-
9
-
-
84897460299
-
ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis
-
btt665
-
Duchêne S., Molak M., Ho S.Y.W. ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. Bioinformatics 2014, btt665.
-
(2014)
Bioinformatics
-
-
Duchêne, S.1
Molak, M.2
Ho, S.Y.W.3
-
10
-
-
37549027209
-
GEIGER: investigating evolutionary radiations
-
Harmon L.J., Weir J.T., Brock C.D., Glor R.E., Challenger W. GEIGER: investigating evolutionary radiations. Bioinformatics 2008, 24:129-131.
-
(2008)
Bioinformatics
, vol.24
, pp. 129-131
-
-
Harmon, L.J.1
Weir, J.T.2
Brock, C.D.3
Glor, R.E.4
Challenger, W.5
-
11
-
-
67649133122
-
An examination of phylogenetic models of substitution rate variation among lineages
-
Ho S.Y.W. An examination of phylogenetic models of substitution rate variation among lineages. Biol. Lett. 2009, 5:421-424.
-
(2009)
Biol. Lett.
, vol.5
, pp. 421-424
-
-
Ho, S.Y.W.1
-
12
-
-
77956087396
-
Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks
-
Ho S.Y.W., Lanfear R. Improved characterisation of among-lineage rate variation in cetacean mitogenomes using codon-partitioned relaxed clocks. Mitochondrial DNA 2010, 21:138-146.
-
(2010)
Mitochondrial DNA
, vol.21
, pp. 138-146
-
-
Ho, S.Y.W.1
Lanfear, R.2
-
14
-
-
84861380450
-
PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses
-
Lanfear R., Calcott B., Ho S.Y.W., Guindon S. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 2012, 29:1695-1701.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1695-1701
-
-
Lanfear, R.1
Calcott, B.2
Ho, S.Y.W.3
Guindon, S.4
-
15
-
-
2442581218
-
The importance of proper model assumption in Bayesian phylogenetics
-
Lemmon A.R., Moriarty E.C. The importance of proper model assumption in Bayesian phylogenetics. Syst. Biol. 2004, 53:265-277.
-
(2004)
Syst. Biol.
, vol.53
, pp. 265-277
-
-
Lemmon, A.R.1
Moriarty, E.C.2
-
16
-
-
37549001784
-
A general comparison of relaxed molecular clock models
-
Lepage T., Bryant D., Philippe H., Lartillot N. A general comparison of relaxed molecular clock models. Mol. Biol. Evol. 2007, 24:2669-2680.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 2669-2680
-
-
Lepage, T.1
Bryant, D.2
Philippe, H.3
Lartillot, N.4
-
17
-
-
79955364420
-
Evaluation of Bayesian models of substitution rate evolution-parental guidance versus mutual independence
-
Linder M., Britton T., Sennblad B. Evaluation of Bayesian models of substitution rate evolution-parental guidance versus mutual independence. Syst. Biol. 2011, 60:329-342.
-
(2011)
Syst. Biol.
, vol.60
, pp. 329-342
-
-
Linder, M.1
Britton, T.2
Sennblad, B.3
-
18
-
-
72049096137
-
Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees
-
Marshall D.C. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Syst. Biol. 2010, 59:108-117.
-
(2010)
Syst. Biol.
, vol.59
, pp. 108-117
-
-
Marshall, D.C.1
-
19
-
-
33845446297
-
Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors
-
Marshall D.C., Simon C., Buckley T.R. Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors. Syst. Biol. 2006, 55:993-1003.
-
(2006)
Syst. Biol.
, vol.55
, pp. 993-1003
-
-
Marshall, D.C.1
Simon, C.2
Buckley, T.R.3
-
20
-
-
1042304216
-
APE: analyses of phylogenetics and evolution in R language
-
Paradis E., Claude J., Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 2004, 20:289-290.
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
21
-
-
67349118917
-
Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny
-
Phillips M.J. Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene 2009, 441:132-140.
-
(2009)
Gene
, vol.441
, pp. 132-140
-
-
Phillips, M.J.1
-
22
-
-
84907095419
-
R: a language and environment for statistical computing.
-
R Core Team,
-
R Core Team, 2008. R: a language and environment for statistical computing. R Found. Stat. Comput.
-
(2008)
R Found. Stat. Comput.
-
-
-
24
-
-
45849092503
-
High rates of molecular evolution in hantaviruses
-
Ramsden C., Melo F.L., Figueiredo L.M., Holmes E.C., Zanotto P.M.A. High rates of molecular evolution in hantaviruses. Mol. Biol. Evol. 2008, 25:1488-1492.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 1488-1492
-
-
Ramsden, C.1
Melo, F.L.2
Figueiredo, L.M.3
Holmes, E.C.4
Zanotto, P.M.A.5
-
25
-
-
84860109324
-
MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space
-
Ronquist F., Teslenko M., van der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A., Huelsenbeck J.P. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 2012, 61:539-542.
-
(2012)
Syst. Biol.
, vol.61
, pp. 539-542
-
-
Ronquist, F.1
Teslenko, M.2
van der Mark, P.3
Ayres, D.L.4
Darling, A.5
Höhna, S.6
Larget, B.7
Liu, L.8
Suchard, M.A.9
Huelsenbeck, J.P.10
-
26
-
-
0036135468
-
Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach
-
Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 2002, 19:101-109.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 101-109
-
-
Sanderson, M.J.1
-
27
-
-
79951548848
-
Phangorn: phylogenetic analysis in R
-
Schliep K.P. Phangorn: phylogenetic analysis in R. Bioinformatics 2011, 27:592-593.
-
(2011)
Bioinformatics
, vol.27
, pp. 592-593
-
-
Schliep, K.P.1
-
28
-
-
28944450584
-
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
-
Shapiro B., Rambaut A., Drummond A.J. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol. 2006, 23:7-9.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 7-9
-
-
Shapiro, B.1
Rambaut, A.2
Drummond, A.J.3
-
30
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
Thorne J.L., Kishino H., Painter I.S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 1998, 15:1647-1657.
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 1647-1657
-
-
Thorne, J.L.1
Kishino, H.2
Painter, I.S.3
-
31
-
-
84857233832
-
Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae
-
Thornhill A.H., Popple L.W., Carter R.J., Ho S.Y.W., Crisp M.D. Are pollen fossils useful for calibrating relaxed molecular clock dating of phylogenies? A comparative study using Myrtaceae. Mol. Phylogenet. Evol. 2012, 63:15-27.
-
(2012)
Mol. Phylogenet. Evol.
, vol.63
, pp. 15-27
-
-
Thornhill, A.H.1
Popple, L.W.2
Carter, R.J.3
Ho, S.Y.W.4
Crisp, M.D.5
-
32
-
-
20144362109
-
Molecular dating when rates vary
-
Welch J.J., Bromham L. Molecular dating when rates vary. Trends Ecol. Evol. 2005, 20:320-327.
-
(2005)
Trends Ecol. Evol.
, vol.20
, pp. 320-327
-
-
Welch, J.J.1
Bromham, L.2
-
33
-
-
72049088557
-
Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference
-
Wertheim J.O., Sanderson M.J., Worobey M., Bjork A. Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference. Syst. Biol. 2010, 59:1-8.
-
(2010)
Syst. Biol.
, vol.59
, pp. 1-8
-
-
Wertheim, J.O.1
Sanderson, M.J.2
Worobey, M.3
Bjork, A.4
-
34
-
-
84873603201
-
Bayesian selection of nucleotide substitution models and their site assignments
-
Wu C.-H., Suchard M.A., Drummond A.J. Bayesian selection of nucleotide substitution models and their site assignments. Mol. Biol. Evol. 2013, 30:669-688.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 669-688
-
-
Wu, C.-H.1
Suchard, M.A.2
Drummond, A.J.3
-
35
-
-
2342590478
-
Molecular disease, evolution and genetic heterogeneity.
-
Kasha, M., Pullman, B. (Eds.), New York.
-
Zuckerkandl, E., Pauling, L., 1962. Molecular disease, evolution and genetic heterogeneity. In: Kasha, M., Pullman, B. (Eds.), New York.
-
(1962)
-
-
Zuckerkandl, E.1
Pauling, L.2
|