The Warnow Lab
Research
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The Warnow Lab works on developing new methods for alignment estimation, phylogeny estimation, and species identification of metagenomic data (short reads). We also work in computational historical linguistics, which involves the development of methods for estimating evolutionary histories of languages and of models of language evolution.

The estimation of phylogenetic trees for biomolecular sequences and multiple sequence alignments are related, because both trees and alignments are hypotheses of the evolutionary history of a set of sequences. Almost all good approaches to multiple sequence alignment or gene tree estimation are NP-hard, leading to the need for very good heuristics, in order to be able to analyze large datasets.

The estimation of the evolutionary history of a set of species involves additional complexity, due to processes (such as horizontal gene transfer, gene duplication and loss, and incomplete lineage sorting) that can lead to discordance between gene trees. The resultant species tree or network estimation problems are also NP-hard, and the best methods are not yet able to run on even moderately large datasets.

The advent of next generation sequencing technologies, estimating trees and alignments has led to huge amounts of data, but even harder estimation problems, due to incomplete sequences (instead of full-length gene sequences).

Metagenomic data analyses bring additional complexity because the datasets contain fragmentary samples from different genes and different species, and even identifying the species that the fragments come from is challenging.

The Warnow Lab develops methods for these problems, focusing on the development of methods that can produce highly accurate results for large datasets. All software developed by the Warnow Lab is open-source.

Our main focus now is on the following topics (see this page of current projects for more information):

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