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3 is now available of our evolutionary analysis of the complete genomes
of oomycetes and diatoms. This now adds the genome of Pythium ultimum
to that of the four previously included oomycete genomes (Phytophthora
sojae, P. ramorum, P. infestans, and Hyaloperonospora
arabidopsidis) and two diatoms (Thalassiosira pseudonana and
Users can see the multiple
sequence alignments and phylogenetic trees of all genes, compare intron-exon
structures, and see maps of the relative arrangements of homologous genes
across all genomes.
Learn more about the methods used here.
Results can be seen here.
In addition, this version includes many updates to the process and presentation, including rewriting nearly all of the code for greater efficiency, changing dependencies from identity scores to distance scores, which can be calculated in a more sophisticated way, and refining of the way that alignment gaps are handled and colinearity of homologous genes is presente
The initial development of PHRINGE was created as part of the project "Phytophthora sojae: A High Quality Reference Sequence for the Oomycetes", directed by Brett Tyler of the Virginia Bioinformatics Institute, and funded by the U.S. National Science Foundation / U.S. Department of Agriculture Microbial Genome Sequencing Program.
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