GapCoder automates the use of indel characters in phylogenetic analysis
<p>Abstract</p> <p>Background</p> <p>Several 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...
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doaj-a27b2eedb3dc4d66bbf6369e7e51cec22020-11-25T00:36:17ZengBMCBMC Bioinformatics1471-21052003-02-0141610.1186/1471-2105-4-6GapCoder automates the use of indel characters in phylogenetic analysisHealy JohnYoung Nelson D<p>Abstract</p> <p>Background</p> <p>Several 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.</p> <p>Algorithm</p> <p>We 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.</p> <p>Discussion</p> <p>Manual 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 <url>http://www.home.duq.edu/~youngnd/GapCoder</url>.</p> http://www.biomedcentral.com/1471-2105/4/6 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Healy John Young Nelson D |
spellingShingle |
Healy John Young Nelson D GapCoder automates the use of indel characters in phylogenetic analysis BMC Bioinformatics |
author_facet |
Healy John Young Nelson D |
author_sort |
Healy John |
title |
GapCoder automates the use of indel characters in phylogenetic analysis |
title_short |
GapCoder automates the use of indel characters in phylogenetic analysis |
title_full |
GapCoder automates the use of indel characters in phylogenetic analysis |
title_fullStr |
GapCoder automates the use of indel characters in phylogenetic analysis |
title_full_unstemmed |
GapCoder automates the use of indel characters in phylogenetic analysis |
title_sort |
gapcoder automates the use of indel characters in phylogenetic analysis |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2003-02-01 |
description |
<p>Abstract</p> <p>Background</p> <p>Several 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.</p> <p>Algorithm</p> <p>We 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.</p> <p>Discussion</p> <p>Manual 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 <url>http://www.home.duq.edu/~youngnd/GapCoder</url>.</p> |
url |
http://www.biomedcentral.com/1471-2105/4/6 |
work_keys_str_mv |
AT healyjohn gapcoderautomatestheuseofindelcharactersinphylogeneticanalysis AT youngnelsond gapcoderautomatestheuseofindelcharactersinphylogeneticanalysis |
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