Abstract
Broad availability of molecular sequence data allows construction of phylogenetic trees with 1000s or even 10 000s of taxa. This paper reviews methodological, technological and empirical issues raised in phylogenetic inference at this scale. Numerous algorithmic and computational challenges have been identified surrounding the core problem of reconstructing large trees accurately from sequence data, but many other obstacles, both upstream and downstream of this step, are less well understood. Before phylogenetic analysis, data must be generated de novo or extracted from existing databases, compiled into blocks of homologous data with controlled properties, aligned, examined for the presence of gene duplications or other kinds of complicating factors, and finally, combined with other evidence via supermatrix or supertree approaches. After phylogenetic analysis, confidence assessments are usually reported, along with other kinds of annotations, such as clade names, or annotations requiring additional inference procedures, such as trait evolution or divergence time estimates. Prospects for partial automation of large-tree construction are also discussed, as well as risks associated with 'outsourcing' phylogenetic inference beyond the systematics community.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 287-301 |
| Number of pages | 15 |
| Journal | Australian Systematic Botany |
| Volume | 20 |
| Issue number | 4 |
| DOIs | |
| State | Published - 2007 |
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ASJC Scopus subject areas
- Plant Science
Cite this
L. A. S. Johnson review no. 9. Construction and annotation of large phylogenetic trees. / Sanderson, Michael.
In: Australian Systematic Botany, Vol. 20, No. 4, 2007, p. 287-301.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - L. A. S. Johnson review no. 9. Construction and annotation of large phylogenetic trees
AU - Sanderson, Michael
PY - 2007
Y1 - 2007
N2 - Broad availability of molecular sequence data allows construction of phylogenetic trees with 1000s or even 10 000s of taxa. This paper reviews methodological, technological and empirical issues raised in phylogenetic inference at this scale. Numerous algorithmic and computational challenges have been identified surrounding the core problem of reconstructing large trees accurately from sequence data, but many other obstacles, both upstream and downstream of this step, are less well understood. Before phylogenetic analysis, data must be generated de novo or extracted from existing databases, compiled into blocks of homologous data with controlled properties, aligned, examined for the presence of gene duplications or other kinds of complicating factors, and finally, combined with other evidence via supermatrix or supertree approaches. After phylogenetic analysis, confidence assessments are usually reported, along with other kinds of annotations, such as clade names, or annotations requiring additional inference procedures, such as trait evolution or divergence time estimates. Prospects for partial automation of large-tree construction are also discussed, as well as risks associated with 'outsourcing' phylogenetic inference beyond the systematics community.
AB - Broad availability of molecular sequence data allows construction of phylogenetic trees with 1000s or even 10 000s of taxa. This paper reviews methodological, technological and empirical issues raised in phylogenetic inference at this scale. Numerous algorithmic and computational challenges have been identified surrounding the core problem of reconstructing large trees accurately from sequence data, but many other obstacles, both upstream and downstream of this step, are less well understood. Before phylogenetic analysis, data must be generated de novo or extracted from existing databases, compiled into blocks of homologous data with controlled properties, aligned, examined for the presence of gene duplications or other kinds of complicating factors, and finally, combined with other evidence via supermatrix or supertree approaches. After phylogenetic analysis, confidence assessments are usually reported, along with other kinds of annotations, such as clade names, or annotations requiring additional inference procedures, such as trait evolution or divergence time estimates. Prospects for partial automation of large-tree construction are also discussed, as well as risks associated with 'outsourcing' phylogenetic inference beyond the systematics community.
UR - http://www.scopus.com/inward/record.url?scp=34548403121&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=34548403121&partnerID=8YFLogxK
U2 - 10.1071/SB07006
DO - 10.1071/SB07006
M3 - Article
AN - SCOPUS:34548403121
VL - 20
SP - 287
EP - 301
JO - Australian Systematic Botany
JF - Australian Systematic Botany
SN - 1030-1887
IS - 4
ER -