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| File | Date | Author | Commit |
|---|---|---|---|
| .idea | 2019-12-22 |
Evys Ancede Gallardo
|
[6fc907] Change Biopython option to subprocess to run bl... |
| calculate | 2019-12-22 |
Evys Ancede Gallardo
|
[6a6e60] Round option changed |
| examples | 2019-09-16 |
Evys Ancede Gallardo
|
[07eead] Modifications of GUI and author format change o... |
| ui | 2019-09-16 |
Evys Ancede Gallardo
|
[d88a3b] Cherry Picking at merge and matrix plot impleme... |
| .gitignore | 2019-12-22 |
Evys Ancede Gallardo
|
[3eaef7] GUI modifications and all matrix calculations f... |
| LICENSE | 2019-09-16 |
eancedeg
|
[102cd7] Create LICENSE |
| README.md | 2020-01-09 |
eancedeg
|
[8c45b0] Authors and bibliographical references modifica... |
| SeqDivA.py | 2019-12-22 |
Evys Ancede Gallardo
|
[470b14] Revert "Change Biopython option to subprocess t... |
| requirements.txt | 2019-12-22 |
Evys Ancede Gallardo
|
[3eaef7] GUI modifications and all matrix calculations f... |
Read Me
SeqDivA
Sequence Diversity Analysis
Authors
- Evys Ancede-Gallardo (eancedeg@gmail.com)
- Guillermin Agüero-Chapin (gaguero@gmail.com)
Sequence Diversity Analysis - SeqDivA version 1.0 is a python-based tool with a friendly GUI designed for Linux and Mac OS.
Utility: Run alignment algorithms (water, needle, and blast) to compare all-vs.-all protein, DNA, and RNA sequences. SeqDivA provides similarity, identity, and bit-score matrixes and dot plots to explore/illustrate the diversity (homology degree) of the sequences, enabling the delimitation of the twilight zone.
Installation Prerequisites:
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matplotlib
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numpy
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pandas
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pyqt
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biopython
Installation:
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Download SeqDivA at https://github.com/eancedeg/SeqDivA
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decompress the “.zip or tar.gz” file
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Load the graphical interface by executing python SeqDivA.py. Python 3.7 is recommended.
Authors:
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Evys Ancede-Gallardo (eancedeg@gmail.com), Programa de Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andrés Bello, Av. República 275, Santiago 8370146, Chile.
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Guillermin Agüero-Chapin (gaguero@gmail.com), CIIMAR- Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Portugal
Reference: Agüero-Chapin, G., Galpert, D., Molina-Ruiz, R., Ancede-Gallardo, E., Pérez-Machado, G., De la Riva, G. A., & Antunes, A. (2019). Graph Theory-Based Sequence Descriptors as Remote Homology Predictors. Biomolecules, 10(1), 26. https://doi.org/10.3390/biom10010026
