Melbourne Systematics Forum

A discussion group for topics in ecology, systematics and evolution

hosted by Museum Victoria Sciences Department

Recent topics - On Alignment and Optimisation

On 7 August 2003, Niels Klazenga from the Royal Botanic Gardens, Melbourne presented a detailed discussion titled On Alignment and Optimisation.
Alignment of DNA sequences is an important step in phylogenetic analysis, as it is during this step that assessments of primary homology are made. Alignment used to be and still is done mostly manually, but recently (or not so recently) various methods have become available that can automate this step. 'Multiple alignment' (implemented in for instance CLUSTALW and MALIGN) provides an alignment that can be submitted to cladistic analysis, while 'direct optimisation' (implemented in POY) directly optimises sequences on trees, inserting gaps where appropriate, while trying to find the most parsimonious tree(s). The idea behind most of these methods is that the best alignment is the one that produces the shortest trees.

I will briefly describe the different methods of alignment and the differences between them. Issues that will come up and may be discussed are, among others, testability of alignments and trees, treatment of gaps and treatment of sites where alignment is ambiguous.

Gatesy, J., R. DeSalle, & W.C. Wheeler (1993). Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Molecular Phylogenetics and Evolution 2, 152-157.
Giribet, G. & W.C. Wheeler (1999). On gaps. Molecular Phylogenetics and Evolution 13, 132-143.
Giribet, G. (2001). Exploring the behavior of POY, a program for direct optimization of molecular data. Cladistics 17, S60-S70.
Phillips, A., D. Janies & W.C. Wheeler (2000). Multiple alignment in phylogenetic analysis. Molecular Phylogenetics and Evolution 16, 317-330.
Wheeler, W.C. (1995). Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Systematic Biology 44, 321-331.
Wheeler, W.C. (1996). Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12, 1-9.
Wheeler, W.C. (1999). Fixed character states and the optimization of molecular sequence data. Cladistics 15, 379-385.
Wheeler, W.C. (2000). Heuristic reconstruction hypothetical-ancestral DNA sequences: sequence alignment vs direct optimization. In: Scotland, R. & R.T. Pennington (eds.), Homology and Systematics, pp. 106-113. The Systematics Association Special Volume Series 58. Taylor & Francis, London.
Wheeler, W.C. (2001). Homology and the optimization of DNA sequence data. Cladistics 17, S3-S11.

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The Melbourne Systematics Forum provides an opportunity for students, academics and others with an interest in systematic biology and related topics to discuss their research results and current ideas in an informal environment. Unless advised otherwise, meetings take place in The Discovery Centre, (previously called InfoZone) lower ground floor, Melbourne Museum, Carlton Gardens, at 6 pm on the first Thursday of the month. Sessions commence with an introduction from the convenor, followed by an informal talk for about 20 minutes. Participants are encouraged to intervene and generate discussion. Meetings generally conclude after about 90 minutes, and everyone who attends a session is encouraged to actively participate.

	Melbourne Systematics Forum A discussion group for topics in ecology, systematics and evolution
	hosted by Museum Victoria Sciences Department
next meeting	Recent topics - On Alignment and Optimisation On 7 August 2003, Niels Klazenga from the Royal Botanic Gardens, Melbourne presented a detailed discussion titled On Alignment and Optimisation. Alignment of DNA sequences is an important step in phylogenetic analysis, as it is during this step that assessments of primary homology are made. Alignment used to be and still is done mostly manually, but recently (or not so recently) various methods have become available that can automate this step. 'Multiple alignment' (implemented in for instance CLUSTALW and MALIGN) provides an alignment that can be submitted to cladistic analysis, while 'direct optimisation' (implemented in POY) directly optimises sequences on trees, inserting gaps where appropriate, while trying to find the most parsimonious tree(s). The idea behind most of these methods is that the best alignment is the one that produces the shortest trees. I will briefly describe the different methods of alignment and the differences between them. Issues that will come up and may be discussed are, among others, testability of alignments and trees, treatment of gaps and treatment of sites where alignment is ambiguous. Gatesy, J., R. DeSalle, & W.C. Wheeler (1993). Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Molecular Phylogenetics and Evolution 2, 152-157. Giribet, G. & W.C. Wheeler (1999). On gaps. Molecular Phylogenetics and Evolution 13, 132-143. Giribet, G. (2001). Exploring the behavior of POY, a program for direct optimization of molecular data. Cladistics 17, S60-S70. Phillips, A., D. Janies & W.C. Wheeler (2000). Multiple alignment in phylogenetic analysis. Molecular Phylogenetics and Evolution 16, 317-330. Wheeler, W.C. (1995). Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Systematic Biology 44, 321-331. Wheeler, W.C. (1996). Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12, 1-9. Wheeler, W.C. (1999). Fixed character states and the optimization of molecular sequence data. Cladistics 15, 379-385. Wheeler, W.C. (2000). Heuristic reconstruction hypothetical-ancestral DNA sequences: sequence alignment vs direct optimization. In: Scotland, R. & R.T. Pennington (eds.), Homology and Systematics, pp. 106-113. The Systematics Association Special Volume Series 58. Taylor & Francis, London. Wheeler, W.C. (2001). Homology and the optimization of DNA sequence data. Cladistics 17, S3-S11. Return to recent topics page.
the venue
2010 meeting calendar
conferences
recent topics
societies and other links
contact the organisers
previous meetings	The Melbourne Systematics Forum provides an opportunity for students, academics and others with an interest in systematic biology and related topics to discuss their research results and current ideas in an informal environment. Unless advised otherwise, meetings take place in The Discovery Centre, (previously called InfoZone) lower ground floor, Melbourne Museum, Carlton Gardens, at 6 pm on the first Thursday of the month. Sessions commence with an introduction from the convenor, followed by an informal talk for about 20 minutes. Participants are encouraged to intervene and generate discussion. Meetings generally conclude after about 90 minutes, and everyone who attends a session is encouraged to actively participate.