GapCoder automates the use of indel characters in phylogenetic analysis

By Nelson D. Young, John Healy. BMC Bioinformatics, 2003

423 citations recorded by the source corpus.

BackgroundSeveral ways of incorporating indels into phylogenetic analysis have been suggested. Simple indel coding has two strengths: (1) biological realism and (2) efficiency of analysis. In the method, each indel with different start and/or end positions is considered to be a separate character. The presence/absence of these indel characters is then added to the data set.AlgorithmWe have written a program, GapCoder to automate this procedure. The program can input PIR format aligned datasets, find the indels and add the indel-based characters. The output is a NEXUS format file, which includes a table showing what region each indel characters is based on. If regions are excluded from analysis, this table makes it easy to identify the corresponding indel characters for exclusion.DiscussionManual implementation of the simple indel coding method can be very time-consuming, especially in data sets where indels are numerous and/or overlapping. GapCoder automates this method and is therefore particularly useful during procedures where phylogenetic analyses need to be repeated many times, such as when different alignments are being explored or when various taxon or character sets are being explored. GapCoder is currently available for Windows from http://www.home.duq.edu/~youngnd/GapCoder.

Subfields: Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/31ec8dc2d5964d8143c4d756d6c2fb1b6dd06e5f

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In Molecular Biology

1. Gerard Talavera
2. A. Phillips
3. Mingai Li
4. Anne Bruneau
5. Julian R. Starr
6. Julio Rozas
7. S. Joly
8. A. Alves

In Paleontology

1. Gerard Talavera
2. Mingai Li
3. Anne Bruneau
4. Julian R. Starr
5. Julio Rozas
6. S. Joly
7. A. Alves
8. C. Varotto

Citations in the corpus

• Evolution and Circumscription of the True Cypresses (Cupressaceae: Cupressus) (2006, methodology): “Characters to describe hypothesized insertion/deletion (indel) events were coded using the simple indel coding method of Simmons and Ochoterena (2000) as implemented in GapCoder (Young and Healy 2003).”
• Central Asian origin of and strong genetic differentiation among populations of the rare and disjunct Carex atrofusca (Cyperaceae) in the Alps (2006, methodology): “Inferred insertions/ deletions (indels) were coded using simple gap coding (Simmons & Ochoterena, 2000) as implemented in GAPCODER (Young & Healy, 2003).”
• An ITS phylogeny of tribe Senecioneae (Asteraceae) and a new delimitation of Senecio L. (2007, methodology): “GapCoder (Young & Healy, 2003) was employed to code insertion/deletion events (indels) as binary characters for their presence or absence using the “simple indel coding method” for recoding of gaps (Simmons & Ochoterena, 2000).”
• DnaSP v5: a software for comprehensive analysis of DNA polymorphism data (2009, background): “One obstacle has been the difficulty of defining clearly homologous states (Young and Healy, 2003).”
• Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum (2009, methodology): “All indels were coded as binary states (0 or 1) by the gapcoder program (Young & Healy, 2003).”
• Diplodia seriata, the anamorph of "Botryosphaeria" obtusa (2007, methodology): “Phylogenetic information contained in indels (gaps) was incorporated into the phylogenetic analysis using simple indel coding as implemented by GapCoder (Young and Healy, 2003).”
• Phylogenetic Relationships in the Genus Rosa: New Evidence from Chloroplast DNA Sequences and an Appraisal of Current Knowledge (2007, methodology): “Searches were performed with both the inclusion and exclusion of indels as coded by GapCoder (Young and Healy 2003), a program that scores gaps according to the simple gap-coding method of Simmons and Ochoterena (2000).”
• PHYLOGENY OF APOCYNOIDEAE AND THE APSA CLADE (APOCYNACEAE S.L.)1 (2007, methodology): “Alignments were constructed manually using Se-Al v. 2.011a (Rambaut, 1996) and indels coded using the simple indel coding method (Simmons & Ochoterena, 2000) as implemented in GapCoder (Young & Healy, 2003).”
• Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. (2007, background): “A third, intermediate option, is the recoding of such regions us-ing different strategies (Geiger, 2002; Lutzoni et al., 2000; Young and Healy, 2003), which allows the use of at least part of the information.”
• Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species (2008, methodology): “The analysis of the indel structure resulting from the alignment procedure was carried out with the help of GapCoder (Young and Healy, 2003).”