Data from: A Poissonian model of indel rate variation for phylogenetic tree inference

We describe a method to construct phylogeny estimates from a fixed alignment using neighbor joining. Using simulation studies, we show that ignoring indel rate variation may have a detrimental effect on the accuracy of the inferred phylogenies, and that our proposed method can sidestep this issue by inferring latent indel rate categories. We also show that our phylogenetic inference method may be more stable to taxa subsampling than methods that either ignore indels or indel rate variation.

Usage notes

Molluscan RNA data This dataset is obtained from rna.icmb.utexas.edu/SIM/4D/Mollusk/alignment.gb. This dataset in nexus format is converted from the original dataset in GenBank format using EMBOSS. The dataset in fasta format used in the data analysis section of the paper can be obtained directly from github.com/yzhai220/geopip together with the source code. molluscan.nexus.txt