Phylogeny Resource page
FYP 1 - PhyloGenie: A Generic Phylogenetic Inference Framework with GPU Compatibility
Dataset :
NCBI : https://www.ncbi.nlm.nih.gov
TreeBASE : https://treebase.org
Balibase : http://www.lbgi.fr/balibase/
Kaggle : https://www.kaggle.com
Genome Bioinformatics Research lab : http://genome.crg.es/datasets
Moshiri N, Mirarab S (2018) A two-state model of tree evolution and its applications to Alu retrotransposition. Systematic Biology 67(3): 475-489. : https://doi.org/10.1093/sysbio/syx088
Moshiri N, Mirarab S (2017) Data from: A two-state model of tree evolution and its applications to alu retrotransposition. Dryad Digital Repository : https://doi.org/10.5061/dryad.13n52
Techniques and Tools:
MUSCLE : https://www.drive5.com/muscle/
MStatX : https://github.com/gcollet/MstatX
Maximum likelihood
NVIDIA CUDA
PHYLIP package
Data for SUS
PhyloGenie - User Manual
PhyloGenie - Task list for SUS
FYP 2 - Dynamic Phylogenetic Tree Construction using LSH and k-mers
Datasets:
Genomic Datasets - Used for Comparisons in ICTer2019 publication
Publically available at https://www.ncbi.nlm.nih.gov/genome/
Genomes of Bolivian Squirrel Monkey https://www.ncbi.nlm.nih.gov/genome/?term=Saimiri_boliviensis_boliviensis
Genomes of Honey Bee https://www.ncbi.nlm.nih.gov/genome/?term=honey+bee
Genomes of American Deer Mouse https://www.ncbi.nlm.nih.gov/genome/?term=Peromyscus_maniculatus
Genomic Datasets - Used for the rest of the project
Genomes of Bacteria ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/
Techniques and Tools:
GATB/DSK tool (Used for k-mer counting) https://github.com/GATB/dsk
Modified LSH algorithm https://en.wikipedia.org/wiki/Locality-sensitive_hashing
Modified K-medoid algorithm https://en.wikipedia.org/wiki/K-medoids