FarmCPU

Dash Bio -- interactive bioinformatics visualization components built on Plotly Dash. Provides domain-specific charts including Circos plots, ideograms, needle plots (lollipop/mutation diagrams), alig

1 shared topic • 3 shared operations

Harvest Tools — core genome phylogenomics suite for rapid whole-genome alignment, SNP extraction, and phylogenetic tree inference from closely related microbial genomes. Parsnp performs MUMmer-based c

1 shared topic • 3 shared operations

IMPUTE5 for genotype imputation from phased haplotypes and a reference panel. Performs fast, accurate imputation using the Li and Stephens hidden Markov model with the PBWT data structure for efficien

1 shared topic • 3 shared operations

GATK HaplotypeCaller — germline short variant caller using localized de novo assembly of haplotypes. Calls SNPs and indels from BAM/CRAM alignment files, producing VCF or gVCF output. Supports single-

1 shared topic • 2 shared operations

OrthoFinder — fast, accurate ortholog inference for comparative genomics. Identifies orthogroups, orthologs, gene trees, rooted species trees, and gene duplication events from protein or nucleotide se

1 shared topic • 2 shared operations