The maximum parsimony (MP) method for inferring phylogenies is widely used, but little is known about its limitations in non-asymptotic situations. This study employs large-scale computations with sim
The data include the following sections: (1) PHLAWD alignments per locus and Genbank identifiers/metadata, (2) RAxML input/output and RogueNaRok output for phylogeny construction, (3) treePL input/out
Phyllogenetic tree (nwk format ) of the 115 single cells (as well as of 5 HLII strains) based on whole-genome sequences (the alignment in file 9:BATS_HOT_ALL_WG_algn.fasta).
Finding the optimal evolutionary history for a set of taxa is a challenging computational problem, even when restricting possible solutions to be âtree-likeâ and focusing on the maximum-parsimony