There are seven workshops available as part of the meeting. There is also a symposium and software school in advance of the meeting, organized by Tandy Warnow: scroll down to see more.
All events in University Union, unless otherwise noted. See floor plans on right side of this page.
Computational Macroevolution: Analysis and Visualization of Complex Evolutionary Dynamics on Phylogenies
8:00 am - 5:00 pm (Union: Kuenzel, 1st floor)
Dan Rabosky
This workshop will focus on the analysis and visualization of macroevolutionary rates on phylogenetic trees using BAMM and BAMMtools. Analyses will include speciation-extinction dynamics as well as phenotypic evolution. The workshop will assume familiarity with the R environment and some prior usage of command line programs. Participants will need to work on their own laptops and should bring at least one suitable data set (time calibrated phylogenies, possibly with trait data) for use during the workshop, although example datasets will be provided. Participants will need to follow instructions on the BAMM project website (bamm-project.org) prior to the workshop to ensure that all software is correctly installed prior to attending.
A number of travel awards (up to $500) are available to defray the cost of registration and housing while attending the conference and this workshop. Applicants to the Computational Macroevolution workshop should email Dan Rabosky ([email protected]) with a brief statement indicating your career stage (e.g., 3rd year PhD student), and a single paragraph that describes why you would like to attend and your previous experience with R and command line programs. Applications must be received by March 20, 2015.
Publishing digital phylogenies: choosing content, formats, repositories and licenses that make trees useful for future work
12:45 pm - 2:45 pm (Union: Pendleton, 2nd floor): Karen Cranston
Students should bring at least one phylogenetic tree - either inferred or downloaded from the web. This module will teach participants how to publish and access phylogenetic data online. We will discuss the benefits of sharing research data, both to you as an author and also to the broader scientific community. Participants will learn how to choose data formats, licenses and repositories for publishing phylogenetic data.
Comparative methods in R
8:00 am - 12:00 pm (Union: Wolverine ABC, 1st floor) Brian O'Meara
This workshop will provide an introduction to R for comparative methods: covering basics of using packages like ape, geiger, OUwie, phytools, and more. The workshop will assume familiarity with the R environment. Participants should bring a research question they want to address and ideally a phylogeny and required data for this question, though this is not required. Students should come with R installed on a laptop as well as the packages listed in the phylogenetics task view on CRAN. Instructions and skeleton code will be available at http://brianomeara.info/Tutorials/ComparativeMethodsInR
Model-based Biogeographical Analyses: Principles and Practice
12:45 pm - 5 pm (Union: Wolverine ABC, 1st floor) Jeet Sukumaran
This workshop will provide a synoptic review of the major approaches to biogoegraphical analyses, with an emphasis on current phylogeny-based computational biogeographical analytical methods. A selection of these approaches will be visited in detail in both theory and practice (e.g., Lagrange, BioGeoBears, BayArea). Students will be expected to have Python 2.7 or later and R 3.0.0 or later installed on their computers before the workshop.
Species-tree estimation from SNPs to sequences
3:00 pm - 5 pm (Union: Pendleton, 2nd floor) Laura Kubatko & Dave Swofford
In this workshop, we will give a brief overview of methods for species tree estimation from sequence and from SNP data, highlighting the different strengths and weaknesses of various classes of methods. The workshop will then focus on understanding the methodology behind the SVDquartets method for species tree inference, which can be applied to both types of data. Finally, we will give a software tutorial on the use of SVDquartets as implemented in the latest release of PAUP*.
* It will be helpful if participants have some familiarity with using PAUP*, though the Mac GUI version will be used for the tutorial and thus the tutorial will be reasonably easy to follow even for those new to PAUP*. Participants should download the most recent version of PAUP* prior to the workshop at http://people.sc.fsu.edu/~dswofford/paup_test/ .
Interogating transcriptomic data from processing to analysis
8:00 am - 12:00 pm (Union: Pendleton, 2nd floor) Stephen Smith
The phylogenomics workshop will focus on basic analyses related to analyzing transcriptomic and genomic data for phylogenetics. In particular, we will examine how to prepare data for phylogenetic analyses, construction of homologs and orthologs, and ways to explore conflict, concordance, and gene duplications.
Bayesian methods for estimating divergence times
8:00 am - 12:00 pm (Angell Hall (Not Union - this is across the street to the left), G115) Tracy Heath
This workshop will introduce models for relaxing the molecular clock, birth-death tree models, and time calibration (particularly using fossils). Bayesian inference methods for performing these analyses will be covered using the software RevBayes as well as BEAST 2. Students should check http://phyloworks.org/resources/ssbws.html for information about required software one week prior to the workshop.
Pre-meeting workshop, May 18-19
A Symposium and Software School focusing on New Methods for Phylogenomics and Metagenomics will be held on May 18-19, immediately preceding the standalone meeting at the University of Michigan. The symposium will cover new methods for multiple sequence alignments, genome-scale species tree estimation, phylogenetic network estimation, and metagenomic taxon identification. The software school will include hands-on tutorials in new methods, and taught by the developers of the software. No fee will be charged.
All events in University Union, unless otherwise noted. See floor plans on right side of this page.
Computational Macroevolution: Analysis and Visualization of Complex Evolutionary Dynamics on Phylogenies
8:00 am - 5:00 pm (Union: Kuenzel, 1st floor)
Dan Rabosky
This workshop will focus on the analysis and visualization of macroevolutionary rates on phylogenetic trees using BAMM and BAMMtools. Analyses will include speciation-extinction dynamics as well as phenotypic evolution. The workshop will assume familiarity with the R environment and some prior usage of command line programs. Participants will need to work on their own laptops and should bring at least one suitable data set (time calibrated phylogenies, possibly with trait data) for use during the workshop, although example datasets will be provided. Participants will need to follow instructions on the BAMM project website (bamm-project.org) prior to the workshop to ensure that all software is correctly installed prior to attending.
A number of travel awards (up to $500) are available to defray the cost of registration and housing while attending the conference and this workshop. Applicants to the Computational Macroevolution workshop should email Dan Rabosky ([email protected]) with a brief statement indicating your career stage (e.g., 3rd year PhD student), and a single paragraph that describes why you would like to attend and your previous experience with R and command line programs. Applications must be received by March 20, 2015.
Publishing digital phylogenies: choosing content, formats, repositories and licenses that make trees useful for future work
12:45 pm - 2:45 pm (Union: Pendleton, 2nd floor): Karen Cranston
Students should bring at least one phylogenetic tree - either inferred or downloaded from the web. This module will teach participants how to publish and access phylogenetic data online. We will discuss the benefits of sharing research data, both to you as an author and also to the broader scientific community. Participants will learn how to choose data formats, licenses and repositories for publishing phylogenetic data.
Comparative methods in R
8:00 am - 12:00 pm (Union: Wolverine ABC, 1st floor) Brian O'Meara
This workshop will provide an introduction to R for comparative methods: covering basics of using packages like ape, geiger, OUwie, phytools, and more. The workshop will assume familiarity with the R environment. Participants should bring a research question they want to address and ideally a phylogeny and required data for this question, though this is not required. Students should come with R installed on a laptop as well as the packages listed in the phylogenetics task view on CRAN. Instructions and skeleton code will be available at http://brianomeara.info/Tutorials/ComparativeMethodsInR
Model-based Biogeographical Analyses: Principles and Practice
12:45 pm - 5 pm (Union: Wolverine ABC, 1st floor) Jeet Sukumaran
This workshop will provide a synoptic review of the major approaches to biogoegraphical analyses, with an emphasis on current phylogeny-based computational biogeographical analytical methods. A selection of these approaches will be visited in detail in both theory and practice (e.g., Lagrange, BioGeoBears, BayArea). Students will be expected to have Python 2.7 or later and R 3.0.0 or later installed on their computers before the workshop.
Species-tree estimation from SNPs to sequences
3:00 pm - 5 pm (Union: Pendleton, 2nd floor) Laura Kubatko & Dave Swofford
In this workshop, we will give a brief overview of methods for species tree estimation from sequence and from SNP data, highlighting the different strengths and weaknesses of various classes of methods. The workshop will then focus on understanding the methodology behind the SVDquartets method for species tree inference, which can be applied to both types of data. Finally, we will give a software tutorial on the use of SVDquartets as implemented in the latest release of PAUP*.
* It will be helpful if participants have some familiarity with using PAUP*, though the Mac GUI version will be used for the tutorial and thus the tutorial will be reasonably easy to follow even for those new to PAUP*. Participants should download the most recent version of PAUP* prior to the workshop at http://people.sc.fsu.edu/~dswofford/paup_test/ .
Interogating transcriptomic data from processing to analysis
8:00 am - 12:00 pm (Union: Pendleton, 2nd floor) Stephen Smith
The phylogenomics workshop will focus on basic analyses related to analyzing transcriptomic and genomic data for phylogenetics. In particular, we will examine how to prepare data for phylogenetic analyses, construction of homologs and orthologs, and ways to explore conflict, concordance, and gene duplications.
Bayesian methods for estimating divergence times
8:00 am - 12:00 pm (Angell Hall (Not Union - this is across the street to the left), G115) Tracy Heath
This workshop will introduce models for relaxing the molecular clock, birth-death tree models, and time calibration (particularly using fossils). Bayesian inference methods for performing these analyses will be covered using the software RevBayes as well as BEAST 2. Students should check http://phyloworks.org/resources/ssbws.html for information about required software one week prior to the workshop.
Pre-meeting workshop, May 18-19
A Symposium and Software School focusing on New Methods for Phylogenomics and Metagenomics will be held on May 18-19, immediately preceding the standalone meeting at the University of Michigan. The symposium will cover new methods for multiple sequence alignments, genome-scale species tree estimation, phylogenetic network estimation, and metagenomic taxon identification. The software school will include hands-on tutorials in new methods, and taught by the developers of the software. No fee will be charged.
