Transcript Genes to Trees Daniel Ayres and Adam Bazinet

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)
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Visual inspection and
post-processing
How does it work?
User inputs:
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Set of DNA or amino acid sequences
Taxonomic constraints
Workflow
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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:
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Phylogenetic tree of closely related organisms
Is it feasible?
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Scripting will be done with Perl
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Extensive use of BioPerl libraries
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Collection of modules for bioinformatics programming
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Accessing sequence data from local and remote databases
Manipulating individual sequences
Searching for similar sequences
Creating and manipulating sequence alignments
Why is this relevant?
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Results can serve as a starting point for further analysis
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Multiple analyses can be run in parallel
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Workflow is modular
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A step towards robust, high-throughput phylogenetics
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