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GapCoder automates the use of indel characters in phylogenetic analysis
1Department of Biological Sciences, Duquesne University, Pittsburgh, PA 15219, USA. youngnd@duq.edu
BMC Bioinformatics
|April 12, 2003
Summary
GapCoder automates simple indel coding for phylogenetic analysis, enhancing biological realism and analytical efficiency. This software simplifies the incorporation of insertions and deletions (indels) into evolutionary studies.
Area of Science:
- Evolutionary biology
- Bioinformatics
Background:
- Phylogenetic analysis traditionally incorporates sequence data.
- Incorporating insertions and deletions (indels) presents challenges.
- Simple indel coding offers biological realism and analytical efficiency.
Purpose of the Study:
- To automate the manual process of simple indel coding.
- To develop a user-friendly program for indel character integration.
Main Methods:
- Developed GapCoder software.
- Input: PIR format aligned datasets.
- Output: NEXUS format file with indel character mapping.
Main Results:
- GapCoder automates the identification and coding of indels.
- Generated NEXUS files include tables for easy exclusion of indel characters.
- Significantly reduces time compared to manual coding.
Conclusions:
- GapCoder streamlines phylogenetic analyses involving numerous or overlapping indels.
- Facilitates iterative analyses, such as exploring different alignments or datasets.
- Available for Windows to aid evolutionary researchers.