diploid

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

snps binary nexus vcf phylogenetics alignment fasta snapp phylip vcf-files polyploid haploid phylogenetic-analysis outgroup convert-snps vcf-format phylip-matrix diploid

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on 3C-based data (Pore-C, CiFi, Hi-C, Omni-C).

genome assembly hi-c scaffolding hic genome-assembly phasing polyploid haplotype-assembly diploid genome-assembler haplotype-resolved-assembly pore-c ultra-long cifi omni-c

Using de-novo assembly and read-phasing to assemble reference-free diploid genomes

Short Sequence Rastreator allows genetic diversity analysis and preparation of input files for other softwares such as STRUCTURE, DARwin and SPAGeDi.

diversity ssr structure dna sequence marker locus genetic loci genomic diploid rosaceae input-files pyrus spagedi triploid

LCVCFtools is a program designed for working with VCF files generated from low-coverage whole genome sequencing

Simulator for the Wright-Fisher model of genetic drift for haploid and diploid populations

This is a modified version of C-Phasing -- zgtools

assembly hi-c scaffolding hic genome-assembly phasing polyploid diploid genome-assembler zgtools

Evolution of a diploid population evolving under a form of viability selection and (optionally) sweepstakes reproduction

evolution selection diploid

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