Phylogenomics Software School at Evolution 2025

Date: June 20 - All Day
Organizers: Tandy Warnow and Siavash Mirarabbaygi
This is part of Evolution 2025; See this page, and note the need to register through Evolution 2025.
Location: Ligotti I and Ligotti 2.

This software school is supported by

the National Science Foundation (grant 2006069),
the Siebel School of Computing and Data Science at the University of Illinois Urbana-Champaign and
the Society for Systematic Biology.

One full day of tutorials and demos covering advances in software related to phylogenomic analysis of large datasets (hundreds to thousands of species and loci). Specific topics will include: inferring multiple sequence alignments, phylogenetic trees for single genes as well as multi-locus datasets, and phylogenetic networks.

Cost: $25
Two coffee breaks are provided
Max capacity: 100
Preregister during registration at Evolution 2025
Please bring a laptop to participate
Target audience: undergraduate students, graduate students, postdocs, faculty, and researchers who estimate alignments and phylogenetic trees or phylogenetic networks, and wish to learn about new advances. People who develop methods are also encouraged to attend.

Software School Program

Tutorials will be presented on Species Tree Estimation (Siavash Mirarab), Phylogenetic Network Estimation (Luay Nakhleh), and Multiple Sequence Alignment (Tandy Warnow). These tutorials will provide a survey of the methods available for these problems, highlighting new methods. We will also have software demos, focusing on methods developed in the last few years. There will be opportunities to work in small groups with the instructors during the coffee breaks. The software that will be discussed (either in the tutorials or in the software demos) will include the following:

Multiple Sequence Alignment

MAGUS: software for large-scale multiple sequence alignment (an improvement on PASTA and SATé). Developer: Vladimir Smirnov. (first paper) (second paper, using recursion) (github) (This will be taught within the tutorial on Multiple Sequence Alignment.)
Twilight: software for large-scale multiple sequence alignment. Developers: Yatish Turakhia and Yu-Hsiang Tseng (UCSD). (github), documentation. Instructor: Yu-Hsiang Tseng. This will be taught in a software demo session.
WITCH: Weighted consensus HMM alignment, a method for aligning large datasets that exhibit sequence length heterogeneity. Developer: Chengze Shen. (paper) (github) This will be discussed in the tutorial on Multiple Sequence Alignment by Tandy Warnow and taught in a software demo session. Instructor: Chengze Shen.

Phylogeny estimation

ASTRAL: software for species tree estimation addressing Incomplete Lineage Sorting. This tutorial will cover installation, input/output formats, annotation, multi-individual usage, ASTRAL-III, ASTRAL-IV, and CASTLES-pro (for branch length estimation). There are multiple software pieces here, with multiple developers. Main Developers: Siavash Mirarab and Chao Zhang, and Yasamin Tabatabaee (for CASTLES-Pro). Papers: ASTRAL, ASTRAL-III, and CASTLES-Pro. This will be discussed in the Species Tree Estimation tutorial by Siavash Mirarab and also taught in a software demo session. Instructor: Shayesteh Arasti, (PhD student at UCSD). (github).
ASTER. This demo will cover advanced tools for species tree estimation, including wASTRAL (i.e., weighted ASTRAL), ASTRAL-Pro (which is for estimating species trees from multi-copy gene trees), CASTLES-Pro (for branch length estimation), and CASTER (software for species tree estimation from site patterns). There are multiple software pieces here, with multiple developers. Main developers: Chao Zhang, Yasamin Tabatabaee (for CASTLES-Pro), and Siavash Mirarab. Papers: CASTER and Weighted ASTRAL. ASTER software will be discussed in the Species Tree Estimation tutorial by Siavash Mirarab and also taught in a software demo session. Instructor: Shayesteh Arasti, (PhD student at UCSD). (github).
DISCO: software for decomposing multi-copy gene family trees into single-copy trees, which can then be used as input to species tree estimation methods like ASTRAL, ASTRID, etc. In addition, the decomposition enables the use of concatenation analyses, using methods like RAxML. Developer: James Willson. (paper) (github) (supplementary materials) Instructor: James Willson. This will be taught during a software demo session.
DupLoss-2M: software for phylogenomic species tree inference using gene tree parsimony. It takes as input a collection of gene trees and seeks a species tree that best reconciles the input gene trees under a gene duplication and loss reconciliation model. DupLoss-2 can lead to significant improvements in species tree reconstruction accuracy compared to other existing methods on phylogenomic datasets where gene duplication and loss are the primary drivers of gene family evolution. DupLoss-2 is scalable to whole-genome datasets with thousands of gene trees from hundreds of taxa. Developer: Mukul Bansal. (paper) (manual) Instructor: Mukul Bansal. This will be taught during a software demo session. (github)
MAPLE: software for pandemic-scale (up to millions of closely related genomes/sequences) maximum likelihood phylogenetic inference. MAPLE can infer a tree, place genomes onto an existing tree, infer mutations and recurrent sequence errors, and assess phylogenetic uncertainty (sprta). Developers: Nicola De Maio and Nhan Ly-Trong. Github for python version. Github site for C++ version. (MAPLE paper). (CMAPLE paper). Instructor: Nicola de Maio. This will be taught within a software demo session.
Phylonet: software for estimating phylogenetic networks. Main developer: Luay Nakhleh. This will be taught within the tutorial on Phylogenetic Network Estimation. (github)
Tree-QMC: Software for quartet-based species tree estimation from gene trees. Its particular strength is robustness to missing data; it also enables quartet weighting to improve robustness to gene tree estimation error. Developers: Yunheng Han and Erin Molloy. github. paper about Tree-QMC paper about weighted Tree-QMC Instructor: Erin Molloy. This will be taught within a software demo session.
SCAMPP and BSCAMPP: software for maximum-likelihood phylogenetic placement into very large trees. BSCAMPP is faster but slightly less accurate, but both can place into very large trees (we have demonstrated this for at least 200,000 leaves). Developer(s): Eleanor Wedell and Chengze Shen. (paper). (github). Instructor: Chengze Shen. This will be taught within a software demo session.

Schedule

8:00-8:45 Coffee provided
8:45-9 Introductory remarks
9-9:45 AM. Tutorial 1: Multiple sequence alignment, taught by Tandy Warnow
9:45-10:15 Coffee Break
10:15-11 Tutorial 2: Species tree estimation, taught by Siavash Mirarabbaygi
11:15-12:00 Tutorial 3: Phylogenetic Network estimation, taught by Luay Nakhleh
12-1:30, Lunch (on your own)
1:30-2:50. Short software demos (WITCH, Twilight, TreeQMC, ASTRAL)
2:50-3:20 Coffee break (and meetings with demo providers)
3:20-5:00 Short software demos (ASTER, DISCO, DupLoss-2M, SCAMPP/BSCAMPP, MAPLE)
5:00-5:10 Closing remarks
5:10-6:00 Closing reception (coffee break with dessert bars and brownies)

Travel Support

My NSF grant 2006069 provides participant support to attendees of the software school, to partially reimburse expenses directly related to attending the software school. Because the participant support funding is limited (just over $9K) and there are potentially 100 attendees, the maximum we can provide to any single individual will be $500. Eligible expenses include accommodations, meals, travel, and the $25 registration fee. Please note: if you are also receiving a travel award from another source, please discuss with me first to plan how to divide the requested reimbursement between the multiple sources.

To apply for travel support (deadline June 25):

Make sure to register for the software school and keep all your receipts for expenses you will request reimbursement for.
You should attend the software school and sign in at the registration desk.
You then submit your receipts and provide required information using this google form
Requests received by June 25 will be given first priority; requests received later (but by June 28) will be considered based on availability of funds. Later requests may not be able to be considered at all, due to the ending of the NSF grant.

Other information

Please see this page for other software schools I will organize. In particular, note the software school Contemporary Challenges in Large-Scale Sequence Alignments and Phylogenies: Bridging Theory and Practice that we are organizing for August 11-14, 2025, at the Institute for Mathematical and Statistical Innovation in Chicago, Illinois. Also, please contact Tandy Warnow (warnow@illinois.edu) for more information.

This software school is supported by the National Science Foundation, through grant 2006069 to Tandy Warnow, IIBR Informatics: Advancing Bioinformatics Methods using Ensembles of Hidden Markov Models"