Genes to Trees Daniel Ayres and Adam Bazinet

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Presentation transcript:

Genes to Trees Daniel Ayres and Adam Bazinet CMSC858P - Project 2 Proposal

Phylogenetic tree reconstruction “Genes to Trees” GenBank Data collection Phylogenetic analysis (PAUP, MrBayes, GARLI) Data curation Multiple sequence alignment (ClustalW, Muscle, MAFFT) Visual inspection and post-processing

How does it work? User inputs: Output: Set of DNA or amino acid sequences Taxonomic constraints Homologous sequences obtained from GenBank Smaller groups eliminated Multiple alignment of each group made Uninformative columns removed “Super-matrix” of all sequences created Phylogenetics analysis performed Output: Phylogenetic tree of closely related organisms Workflow

Is it feasible? Scripting will be done with Perl Extensive use of BioPerl libraries Collection of modules for bioinformatics programming Accessing sequence data from local and remote databases Manipulating individual sequences Searching for similar sequences Creating and manipulating sequence alignments

Why is this relevant? Results can serve as a starting point for further analysis Multiple analyses can be run in parallel Workflow is modular A step towards robust, high-throughput phylogenetics