Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Ploidy agnostic phasing pipeline and algorithm

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.

Method for rescuing collapsed contigs.

Automated processing and haplotype inference for double-barcoded PCR amplicons

🌺 Short pipeline for counting number of clusters across .sam files