Pinned Repositories
cactus
Official home of genome aligner based upon notion of Cactus graphs
Comparative-Annotation-Toolkit
hal
Hierarchical Alignment Format
hal2vg
Convert HAL to VG
mafTools
Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
neutral-model-estimator
Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit
paffy
Small C/CLI library of pairwise alignment format (paf) format tools used by Cactus
SegAlign
A Scalable GPU System for Pairwise Whole Genome Alignments
sonLib
Small general-purpose library for C and Python with an emphasis on bioinformatics.
taffy
This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
ComparativeGenomicsToolkit's Repositories
ComparativeGenomicsToolkit/cactus
Official home of genome aligner based upon notion of Cactus graphs
ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit
ComparativeGenomicsToolkit/hal
Hierarchical Alignment Format
ComparativeGenomicsToolkit/taffy
This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
ComparativeGenomicsToolkit/hal2vg
Convert HAL to VG
ComparativeGenomicsToolkit/neutral-model-estimator
Simple pipeline to go from an alignment to a neutral model, using the PHAST toolkit
ComparativeGenomicsToolkit/mafTools
Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
ComparativeGenomicsToolkit/sonLib
Small general-purpose library for C and Python with an emphasis on bioinformatics.
ComparativeGenomicsToolkit/paffy
Small C/CLI library of pairwise alignment format (paf) format tools used by Cactus
ComparativeGenomicsToolkit/SegAlign
A Scalable GPU System for Pairwise Whole Genome Alignments
ComparativeGenomicsToolkit/pinchesAndCacti
Library for constructing pinch graphs and cactus graphs
ComparativeGenomicsToolkit/cactus-gfa-tools
ComparativeGenomicsToolkit/ComparativeGenomicsToolkit.github.io
ComparativeGenomicsToolkit/kyoto
Kyoto Tycoon key-value store (and the underlying Kyoto Cabinet library)
ComparativeGenomicsToolkit/lastz
Program for aligning DNA sequences, a pairwise aligner.
ComparativeGenomicsToolkit/matchingAndOrdering
Library of matching and ordering algorithms, used for the "reference problem"
ComparativeGenomicsToolkit/RetroFinder
Tool for finding retroposed genes in genomes
ComparativeGenomicsToolkit/hal-grpc-server
ComparativeGenomicsToolkit/quick-tree-check
Fast phylogeny estimation/verification using alignment-free distances.
ComparativeGenomicsToolkit/363-avian-2020-hub
Assembly hub for 363-way avian alignment from 2020
ComparativeGenomicsToolkit/abPOA
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
ComparativeGenomicsToolkit/alignment-annotation-review
ComparativeGenomicsToolkit/cactus2hal
ComparativeGenomicsToolkit/cactusTestData
Datasets required to run cactus unit tests
ComparativeGenomicsToolkit/CAT_paper
ComparativeGenomicsToolkit/cPecan
C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
ComparativeGenomicsToolkit/maf_stream
ComparativeGenomicsToolkit/repeatMaskerPipeline
ComparativeGenomicsToolkit/toil
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
ComparativeGenomicsToolkit/zoonomia-hub
Zoonomia hub