ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis

Abstract

A tooL for Prokaryotic Phylogeny And Clustering Analysis (ALPPACA) is a pipeline that allows both de-novo and reference-based phylogenetic analysis of prokaryotic genomes. The pipeline provides a suite of analyses tailored for different scenarios, designed to allow analysis of datasets represented by three different genetic diversity levels, all in one package. These levels of similarity influence what assumptions are used to consider sequences as orthologous when reconstructing the multiple alignment required for phylogenetic inference. By selecting an appropriate track for the data at hand, the user can be confident that these assumptions are taken care of within the framework of ALPPACA.