SPLACE: A tool to automatically SPLit, Align, and ConcatenatE genes for phylogenomic inference of several organisms

The reconstruction of phylogenomic trees containing multiple genes is best achieved by using a supermatrix. The advent of NGS technology made it easier and cheaper to obtain multiple gene data in one sequencing run. When numerous genes and organisms are used in the phylogenomic analysis, it is difficult to organize all information and manually align the gene sequences to further concatenate them. This study describes SPLACE, a tool to automatically SPLit, Align, and ConcatenatE the genes of all species of interest to generate a supermatrix file, and consequently, a phylogenetic tree, while handling possible missing data. In our findings, SPLACE was the only tool that could automatically align gene sequences and also handle missing data; and, it required only a few minutes to produce a supermatrix FASTA file containing 83 aligned and concatenated genes from the chloroplast genomes of 270 plant species. It is an open-source tool and is publicly available at https://github.com/reinator/splace.