xenoGI
xenoGI is a software tool to identify genomic islands and map the origins of bacteria clades. The xenoGI algorithm includes the reconstruction of the history of gene families, and the package utilizes MUSCLE, FastTree, and GeneRax.
Topic
Genomics;Nucleic acid sites, features and motifs;Microbiology;Phylogeny
Detail
Operation: Phylogenetic tree analysis;Sequence feature detection
Software interface: Web user interface
Language: Python
License: GNU General Public License v3
Cost: Free
Version name: 3.0.0
Credit: HHMI Undergraduate Science Education.
Input: -
Output: -
Contact: Eliot C. Bush bush@hmc.edu
Collection: -
Maturity: Stable
Publications
- xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria.
- Bush EC, Clark AE, DeRanek CA, Eng A, Forman J, Heath K, Lee AB, Stoebel DM, Wang Z, Wilber M, Wu H. xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria. BMC Bioinformatics. 2018 Feb 5;19(1):32. doi: 10.1186/s12859-018-2038-0. PMID: 29402213; PMCID: PMC5799925.
- https://doi.org/10.1186/s12859-018-2038-0
- PMID: 29402213
- PMC: PMC5799925
- Maximum parsimony reconciliation in the DTLOR model.
- Liu J, Mawhorter R, Liu N, Santichaivekin S, Bush E, et al. (2021). Maximum parsimony reconciliation in the DTLOR model. BMC Bioinformatics 22(Suppl 10): 394.
- https://doi.org/10.1186/s12859-021-04290-6
- PMID: 34348661
- PMC: PMC8340394
Download and documentation
Source: https://github.com/ecbush/xenoGI/releases/tag/v3.0.0
Documentation: https://github.com/ecbush/xenoGI/blob/master/TUTORIAL.rst
Home page: https://github.com/ecbush/xenoGI
< Back to DB search