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本文引用的文献
1
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Bioinformatics. 2005 Nov 1;21 Suppl 3:iii31-8. doi: 10.1093/bioinformatics/bti1200.
2
Evolutionary distance estimation and fidelity of pair wise sequence alignment.
BMC Bioinformatics. 2005 Apr 19;6:102. doi: 10.1186/1471-2105-6-102.
3
Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models.
Syst Biol. 2004 Dec;53(6):904-13. doi: 10.1080/10635150490522629.
4
Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree.
J Exp Zool B Mol Dev Evol. 2005 Jan 15;304(1):64-74. doi: 10.1002/jez.b.21026.
5
MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution.
Genome Res. 2004 Mar;14(3):442-50. doi: 10.1101/gr.1571904.
6
Benchmarking tools for the alignment of functional noncoding DNA.
BMC Bioinformatics. 2004 Jan 21;5:6. doi: 10.1186/1471-2105-5-6.
7
Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference.
Mol Biol Evol. 2003 Apr;20(4):610-21. doi: 10.1093/molbev/msg067. Epub 2003 Apr 2.
8
Incomplete taxon sampling is not a problem for phylogenetic inference.
Proc Natl Acad Sci U S A. 2001 Sep 11;98(19):10751-6. doi: 10.1073/pnas.191248498. Epub 2001 Aug 28.
9
Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used.
Mol Biol Evol. 2000 Aug;17(8):1251-8. doi: 10.1093/oxfordjournals.molbev.a026408.
10
Rose: generating sequence families.
Bioinformatics. 1998;14(2):157-63. doi: 10.1093/bioinformatics/14.2.157.
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