title: DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution.
abstract: Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank, and the new NeXML format for interoperability, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony, and maximum-likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot, and many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly, and intuitive interface and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16, 2013).
authors.affiliation: Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, Canada.
authors.forename: Xuhua
authors.initials: X
authors.lastname: Xia
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003062:Codon / Q000235:genetics; D019295:Computational Biology; D019143:Evolution, Molecular; D020440:Gene Duplication / Q000235:genetics; D016678:Genome; D010802:Phylogeny; D016415:Sequence Alignment; D017421:Sequence Analysis; D012984:Software; D013223:Statistics as Topic
chemical_list: D003062:Codon
keywords: Gibbs sampler; bioinformatics; codon usage; dating; genomic analysis; hidden Markov model; motif discovery; phylogenetics; secondary structure
references.citation: Mol Biol Evol. 2002 Jan;19(1):58-67
references.pmid: 11752190
references.citation: Science. 1996 May 3;272(5262):745-6
references.pmid: 8614839
references.citation: Mol Biol Evol. 1995 Sep;12(5):834-42
references.pmid: 7476129
references.citation: Mol Phylogenet Evol. 1995 Sep;4(3):314-30
references.pmid: 8845967
references.citation: PLoS One. 2011 Feb 28;6(2):e17458
references.pmid: 21386988
references.citation: Proc Natl Acad Sci U S A. 2004 Jul 27;101(30):11030-5
references.pmid: 15258291
references.citation: BMC Evol Biol. 2011 Nov 21;11:342
references.pmid: 22103247
references.citation: Science. 2003 Apr 11;300(5617):321-4
references.pmid: 12690198
references.citation: PLoS One. 2011 Mar 18;6(3):e18022
references.pmid: 21437207
references.citation: PLoS One. 2012;7(12):e51652
references.pmid: 23272132
references.citation: Evol Bioinform Online. 2007 May 17;3:53-8
references.pmid: 19461982
references.citation: Cell. 2009 Oct 2;139(1):149-60
references.pmid: 19804760
references.citation: Syst Biol. 2000 Mar;49(1):87-100
references.pmid: 12116485
references.citation: Mol Ecol. 2011 Dec;20(24):5313-27
references.pmid: 22097966
references.citation: Mol Phylogenet Evol. 2012 Mar;62(3):848-55
references.pmid: 22178366
references.citation: J Theor Biol. 2008 Aug 7;253(3):508-13
references.pmid: 18486155
references.citation: Genetics. 1998 May;149(1):37-44
references.pmid: 9584084
references.citation: BMC Evol Biol. 2011 Aug 27;11:246
references.pmid: 21871115
references.citation: Mol Phylogenet Evol. 2003 Jan;26(1):1-7
references.pmid: 12470932
references.citation: Mol Biol Evol. 1998 Mar;15(3):336-44
references.pmid: 9501500
references.citation: Scientifica (Cairo). 2012;2012:917540
references.pmid: 24278755
references.citation: Cytogenet Genome Res. 2003;101(3-4):206-11
references.pmid: 14684984
references.citation: J Mol Biol. 1981 Feb 15;146(1):1-21
references.pmid: 6167728
references.citation: Genetics. 1992 Sep;132(1):269-76
references.pmid: 1398060
references.citation: PLoS One. 2009;4(1):e4136
references.pmid: 19125192
references.citation: Am Nat. 2005 Dec;166(6):776-84
references.pmid: 16475092
references.citation: PLoS One. 2007 Feb 21;2(2):e227
references.pmid: 17311091
references.citation: Nucleic Acids Res. 1987 Feb 11;15(3):1281-95
references.pmid: 3547335
references.citation: Mol Biol Evol. 1997 Nov;14(11):1106-13
references.pmid: 9364768
references.citation: Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8
references.pmid: 3162770
references.citation: BMC Evol Biol. 2008 Jul 19;8:211
references.pmid: 18638409
references.citation: Comp Funct Genomics. 2011;2011:212146
references.pmid: 22162666
references.citation: J Mol Evol. 2008 May;66(5):484-93
references.pmid: 18401633
references.citation: Protein Sci. 1995 Aug;4(8):1618-32
references.pmid: 8520488
references.citation: Mol Biol Evol. 1987 Jul;4(4):406-25
references.pmid: 3447015
references.citation: Nature. 1999 Oct 28;401(6756):877-84
references.pmid: 10553904
references.citation: Mol Biol Evol. 2006 Jul;23(7):1450-4
references.pmid: 16687416
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3429-31
references.pmid: 12824340
references.citation: Genetics. 2002 Aug;161(4):1385-94
references.pmid: 12196387
references.citation: Curr Genomics. 2012 Mar;13(1):16-27
references.pmid: 22942672
references.citation: PLoS One. 2011 Mar 10;6(3):e17512
references.pmid: 21423746
references.citation: Mol Biol Evol. 2013 Jan;30(1):191-6
references.pmid: 22915832
references.citation: J Med Genet. 2002 Dec;39(12):916-21
references.pmid: 12471206
references.citation: Gene. 1990 Mar 1;87(1):23-9
references.pmid: 2110097
references.citation: Mol Biol Evol. 2011 Jun;28(6):1827-34
references.pmid: 21216840
references.citation: J Mol Evol. 1996 Jul;43(1):32-40
references.pmid: 8660427
references.citation: PLoS One. 2012;7(2):e31314
references.pmid: 22348069
references.citation: PLoS One. 2012;7(7):e41754
references.pmid: 22848590
references.citation: Genetics. 1996 Nov;144(3):1309-20
references.pmid: 8913770
references.citation: J Mol Endocrinol. 2004 Dec;33(3):705-15
references.pmid: 15591029
references.citation: J Virol. 2002 Aug;76(16):8298-309
references.pmid: 12134035
references.citation: Syst Biol. 2003 Jun;52(3):283-95
references.pmid: 12775520
references.citation: Syst Biol. 2012 Jul;61(4):675-89
references.pmid: 22357728
references.citation: Evol Bioinform Online. 2007 Feb 26;2:333-45
references.pmid: 19455228
references.citation: Genetics. 2011 Oct;189(2):469-78
references.pmid: 21840854
references.citation: PLoS Comput Biol. 2005 Jun;1(1):e3
references.pmid: 16103904
references.citation: Gene. 2005 Jan 17;345(1):13-20
references.pmid: 15716092
references.citation: J Comput Biol. 2002;9(5):687-705
references.pmid: 12487758
references.citation: PLoS One. 2010 Oct 27;5(10):e13431
references.pmid: 21048949
references.citation: J Mol Evol. 2006 Jul;63(1):120-6
references.pmid: 16786438
references.citation: J Mol Evol. 1998 Nov;47(5):557-64
references.pmid: 9797406
references.citation: BMC Genet. 2005 Apr 11;6:20
references.pmid: 15823202
references.citation: Mol Phylogenet Evol. 2009 Sep;52(3):665-76
references.pmid: 19416757
references.citation: Bioinformatics. 2001 Jun;17(6):569-70
references.pmid: 11395438
references.citation: Mol Phylogenet Evol. 2011 May;59(2):342-53
references.pmid: 21320613
references.citation: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references.pmid: 7984417
references.citation: Mol Biol Evol. 1994 Sep;11(5):715-24
references.pmid: 7968485
references.citation: J Mol Evol. 2003;57 Suppl 1:S21-8
references.pmid: 15008400
references.citation: J Hered. 2001 Jul-Aug;92(4):371-3
references.pmid: 11535656
references.citation: J Mol Evol. 2003 Mar;56(3):362-70
references.pmid: 12612839
references.citation: Comput Appl Biosci. 1994 Feb;10(1):41-8
references.pmid: 8193955
references.citation: PLoS One. 2007 Feb 07;2(2):e188
references.pmid: 17285142
references.citation: Mol Ecol. 2013 Jan;22(1):143-56
references.pmid: 23163335