Genes to Trees Daniel Ayres and Adam Bazinet

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Genes to Trees Daniel Ayres and Adam Bazinet

• CMSC858P - Project 2 Proposal

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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
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How does it work?

• User inputs
• 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
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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

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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