HaplowebMaker and CoMa: Two web tools to delimit species using haplowebs and conspecificity matrices

Abstract

Abstract Haplotype webs (haplowebs) and conspecificity matrices have recently been proposed as graphical methods for species delimitation. However, performing such analyses by hand can be error‐prone and time‐consuming, and no program is currently available to generate these graphs automatically. Here we present two online tools called HaplowebMaker and CoMa (short for ‘Conspecificity Matrices') that fill this gap. Starting from one or several FASTA sequence alignments, HaplowebMaker generates median‐joining (or minimum spanning) networks, then adds connections between sequences found co‐occurring in heterozygous individuals, thereby turning each network into a haploweb. HaplowebMaker also returns a partition matrix summarizing the partitions inferred from each marker using the criterion of mutual allelic exclusivity. CoMa then turns the partition matrix into a conspecificity matrix and orders it, producing a figure in which each species is revealed as a square along the diagonal. HaplowebMaker and CoMa are open source and written in Haxe; webserver implementations are available at https://eeg‐ebe.github.io/HaplowebMaker and https://eeg‐ebe.github.io/CoMa/ .

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