title: TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees.
abstract: Modern phylogenomic analyses often result in large collections of phylogenetic trees representing uncertainty in individual gene trees, variation across genes, or both. Extracting phylogenetic signal from these tree sets can be challenging, as they are difficult to visualize, explore, and quantify. To overcome some of these challenges, we have developed TreeScaper, an application for tree set visualization as well as the identification of distinct phylogenetic signals. GUI and command-line versions of TreeScaper and a manual with tutorials can be downloaded from https://github.com/whuang08/TreeScaper/releases TreeScaper is distributed under the GNU General Public License.
authors.affiliation: Department of Computational and Applied Mathematics, Rice University, St. Housten, TX huwst08@gmail.com.
authors.forename: Wen
authors.initials: W
authors.lastname: Huang
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA.
authors.forename: Guifang
authors.initials: G
authors.lastname: Zhou
authors.affiliation: Department of Mathematics, Florida State University, Tallahassee, FL.
authors.forename: Melissa
authors.initials: M
authors.lastname: Marchand
authors.affiliation: Bioinformatics Research Center, North Carolina State University, Raleigh, NC.
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Ash
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA.
authors.forename: David
authors.initials: D
authors.lastname: Morris
authors.affiliation: Department of Mathematical Engineering, ICTEAM, Université catholique de Louvain, Belgium, Germany.
authors.forename: Paul
authors.initials: P
authors.lastname: Van Dooren
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA.
authors.forename: Jeremy M
authors.initials: JM
authors.lastname: Brown
authors.affiliation: Department of Mathematics, Florida State University, Tallahassee, FL.
authors.forename: Kyle A
authors.initials: KA
authors.lastname: Gallivan
authors.affiliation: Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN.
authors.forename: Jim C
authors.initials: JC
authors.lastname: Wilgenbusch
mesh_terms: D003198:Computer Simulation; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: TreeScaper; community detection; phylogenetic trees.; visualization