Anvaya: phylogenomic analysis of chromosome fusion-and-mixing characters and detection of shared whole-genome duplication

Chromosome-scale conservation of gene linkage (macrosynteny) provides phylogenetic characters largely independent of sequence data. Fusion of ancestral linkage groups, and especially the subsequent interspersion (mixing) of their genes, is argued to be effectively irreversible, and such synapomorphic events have been used to resolve deep, contentious nodes. I present Anvaya, a dependency-light, open-source toolkit of two Python programs with companion threshold-calibration tools which takes reciprocal-best-hit (RBH) synteny data directly to a phylogenetic analysis that codes fusion and mixing as discrete characters under explicit optimality criteria. The syntenybuilder module builds RBH orthology tables from genome assemblies, using either a designated reference genome or a multi-genome consensus procedure that reconstructs linkage groups de novo, requiring no curated reference set. The character-maps module codes every pairwise linkage-group co-occurrence as unfused, fused-clean or fused-and-mixed from gene order and a Fisher's exact test, then searches for the most parsimonious trees under an unordered (Fitch/Sankoff) and an ordered, irreversible (Camin-Sokal) cost model, optionally under a backbone constraint. Every tree is accompanied by ancestral states, synapomorphies mapped onto clades, consistency and retention indices, bootstrap support, and a permutation test of phylogenetic signal. Anvaya also detects whole-genome and segmental duplication from an intragenomic comparison and recovers the ohnologs that reciprocal best hit structurally drops, which can otherwise render a retained linkage group invisible. Outputs include vector figures and matrices in NEXUS and TNT/Hennig86 formats for verification in PAUP* and TNT. On synthetic data, consensus reconstruction resists a conflicting genome, rescue reverses a total false negative, and the diagnostics flag a deliberately homoplastic character. Across thirteen acarine and outgroup genomes, weakly supported associations concentrate in the most distant genome and in poorly assembled regions. In two duplicated chelicerates, ohnolog rescue recovered 12.5% (Limulus polyphemus) and 2.8% (Mastigoproctus giganteus) and restored three Limulus chromosomes that otherwise carried none.