comparativegenomicstoolkit Goto Github PK

363-avian-2020-hub

Assembly hub for 363-way avian alignment from 2020

abpoa

abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

alignment-annotation-review

cactus

Official home of genome aligner based upon notion of Cactus graphs

cactus-gfa-tools

cactus2hal

cactustestdata

Datasets required to run cactus unit tests

cat_paper

cgtbuild

Vuild of Cactus and Comparative Genomics Toolkit

comparative-annotation-toolkit

comparativegenomicstoolkit.github.io

coordination

Coordination of development tasks for the Comparative Genomics Toolkit

cpecan

C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.

hal

Hierarchical Alignment Format

hal-grpc-server

hal2vg

Convert HAL to VG

kyoto

Kyoto Tycoon key-value store (and the underlying Kyoto Cabinet library)

lastz

Program for aligning DNA sequences, a pairwise aligner.

maf_stream

maftools

Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.

matchingandordering

Library of matching and ordering algorithms, used for the "reference problem"

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

pinchesandcacti

Library for constructing pinch graphs and cactus graphs

quick-tree-check

Fast phylogeny estimation/verification using alignment-free distances.

repeatmaskerpipeline

retrofinder

Tool for finding retroposed genes in genomes

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