Phyutility: a phyloinformatics tool for trees, alignments and molecular data

By Stephen A. Smith, Casey W. Dunn. Bioinform., 2008

576 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5e410ad025100890560ed7623559470db36a9eba

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology, Evolution, Behavior and Systematics

1. R. Meier
2. M. Borowiec
3. Gaurav Vaidya
4. David J. Lohman
5. B. Wiegmann
6. T. Pape
7. S. N. Kutty
8. Alexandros Stamatakis

In Genetics

1. Gonzalo Giribet
2. B. Wiegmann
3. G. Edgecombe
4. R. Meier
5. Ward C. Wheeler
6. M. Borowiec
7. T. Pape
8. S. N. Kutty

In Molecular Biology

1. Gonzalo Giribet
2. R. Meier
3. B. Wiegmann
4. T. Pape
5. S. N. Kutty
6. G. Edgecombe
7. Ward C. Wheeler
8. M. Borowiec

Citations in the corpus

• Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly (2010, methodology): “Here we used the leaf stability index (Dunn et al., 2008; Smith & Dunn, 2008) and applied it to jackknife trees based on all data.”
• Assessing the root of bilaterian animals with scalable phylogenomic methods (2009, methodology): “We have addressed this issue by looking at support for relationships between nested subsamples of the most stable taxa, as assessed by leaf stability indices (Thorley & Wilkinson 1999; Smith & Dunn 2008 ).”
• AMAS: a fast tool for alignment manipulation and computing of summary statistics (2016, methodology): “Phyutility also allows for interactions with the NCBI databases and a number of manipulations on phylogenetic trees.”
• SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information (2011, background): “…character and gene files into such sets (e.g. Maddison and Maddison, 2001, 2009; Jones and Blaxter, 2006; Roure et al., 2007; Goloboff et al., 2008; Smith and Dunn, 2008), but the concatenation tools are generally not particularly user-friendly, often do not preserve character set or codon…”
• Angiosperm phylogeny: 17 genes, 640 taxa. (2011, unknown): “Sites in the alignment with more than 50% missing data were removed with the program Phyutility ( Smith and Dunn, 2008 ; see discussion in Castresana, 2000 ) to avoid regions of potentially problematic ambiguous alignment caused by such broad sampling ( Talavera and Castresana, 2007 ).”
• Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits (2018, unknown): “Smith SA, Dunn CW. Phyutility: a phyloinformatics tool for trees, alignments and molecular data.”