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

2. 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

3. 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

4. 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

5. 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