Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods Luay Nakhleh Jerry Sun Tandy Warnow Dept. of Computer Sciences, U. of Texas, Austin, TX 78712 {nakhleh,jsun,tandy}

Source URL: www.cs.rice.edu

1 An overview of phylogeny reconstruction 1.1 Introduction : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 1.2 What are phylogenies used for in biological

Source URL: web.engr.illinois.edu

• Phylogenetics
• Biology
• Outgroup
• Computational phylogenetics
• Molecular phylogenetics
• Phylogenetic tree
• Systematics
• Phylogenetic network
• Species
• Most recent common ancestor
• Lineage
• Horizontal gene transfer

OPTIMIZING PHYLOGENETIC DIVERSITY ACROSS TWO TREES MAGNUS BORDEWICH, CHARLES SEMPLE, AND ANDREAS SPILLNER Abstract. We present a polynomial-time algorithm for finding an optimal set of taxa that maximizes the weighted-su

Source URL: community.dur.ac.uk

• Graph theory
• Mathematics
• Computational complexity theory
• NP-complete problems
• Combinatorial optimization
• Matching
• Flow network
• 3-dimensional matching
• Vertex cover

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

Source URL: tandy.cs.illinois.edu

• Biology
• Phylogenetics
• Computational phylogenetics
• Genetics
• Population genetics
• Bioinformatics
• Horizontal gene transfer
• Phylogenetic network
• Coalescent theory
• Phylogenetic tree
• Sequence alignment
• Species

IEEE TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, VOL. 1, NO. 1,

Source URL: www.cs.unm.edu

• Graph theory
• Phylogenetics
• Mathematics
• Discrete mathematics
• Phylogenetic network
• Phylogenetic tree
• Directed graph
• Unrooted binary tree
• Tree
• Flow network
• B-tree
• Vertex

Computational Phylogenetics An introduction to designing methods for phylogeny estimation Tandy Warnow Contents

Source URL: tandy.cs.illinois.edu

• Computational phylogenetics
• Phylogenetics
• Biology
• Maximum parsimony
• Phylogenetic tree
• Unrooted binary tree
• Sequence alignment
• Tree alignment
• Multiple sequence alignment
• Phylogenetic network
• Disk-covering method
• Supertree

NetworkUser Guide Version date: 24 December 2015 Copyright © 2015 Fluxus Technology Ltd. All rights reserved. Legal Disclaimer :

Source URL: fluxus-technology.com

• Bioinformatics
• Computational phylogenetics
• Biology
• FASTA
• Phylogenetic network
• Sequence alignment
• Transmission Control Protocol
• Mathematical and theoretical biology
• Computer network
• Science

ORIGINAL RESEARCH A Reduction Algorithm for Computing The Hybridization Number of Two Trees Magnus Bordewich 1, Simone Linz 2,3, Katherine St. John 4 and Charles Semple 2 1

Source URL: community.dur.ac.uk

• Phylogenetics
• Knowledge representation
• Data types
• Phylogenetic network
• Agreement forest
• Tree
• Phylogenetic tree
• Reticulate evolution
• Bioinformatics
• Binary trees

Advances in Applied Mathematics–430 www.elsevier.com/locate/yaama Counting consistent phylogenetic trees is #P-complete Magnus Bordewich a,∗ , Charles Semple b , John Talbot c

Source URL: community.dur.ac.uk

• Phylogenetics
• Binary trees
• Tree
• Phylogenetic tree
• Splay tree
• Computational phylogenetics
• Phylogenetic network
• Unrooted binary tree

imperial_college_mike_steel.pptx

Source URL: www.mathtreesworkshop.org.uk

• Phylogenetics
• Knowledge representation
• Phylogenetic network
• Tree
• Binary tree
• Phylogenetic tree
• Spanning tree
• Minimum spanning tree
• Top tree