Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs.

We address the problem of how to estimate a phylogenetic network when given single-nucleotide polymorphisms (i.e., SNPs, or bi-allelic markers that have evolved under the infinite sites assumption).

EMMA: a new method for computing multiple sequence alignments given a constraint subset alignment.

Background: Adding sequences into an existing (possibly user-provided) alignment has multiple applications, including updating a large alignment with new data, adding sequences into a constraint alignment constructed using biological knowledge, or computing alignments in the presence of sequence length heterogeneity. Although this is a natural problem, only a few tools have been developed to use this information with high fidelity.

Results: We present EMMA (Extending Multiple alignments using MAFFT--add) for the problem of adding a set of unaligned sequences into a multiple sequence alignment (i.

Weighted ASTRID: fast and accurate species trees from weighted internode distances.

Background: Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., "gene tree heterogeneity").