Data for: Rapid alignment updating with Extensiphy

1. High throughput sequencing has become commonplace in evolutionary studies. Large, rapidly collected genomic datasets are used to capture biodiversity and for monitoring global and national scale disease transmission patterns, among many other applications. Updating homologous sequence datasets with new samples is cumbersome, requiring excessive program runtimes and data processing. We describe Extensiphy, a bioinformatics tool to efficiently update multiple sequence alignments with whole-genome short-read data. Extensiphy performs reference based sequence assembly and alignment in one process while maintaining the alignment length of the original alignment. Input data- types for Extensiphy are any multiple sequence alignment in fasta format and whole-genome, short-read fastq sequences. 2. To validate Extensiphy, we compared its results to those produced by two other methods that construct whole-genome scale multiple sequence alignments. We measured our comparisons by analyzing pr...