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

  • Ribosomal Database

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

Dataset 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

Research Home Phylogeny Group Publications