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allelefinder

AlleleFinder is a tool for identifying allele genes from polyploid genome.

allhic

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

allhic_components

Some components that speed up and reduce resource cost for original ALLHiC

ancestral_genome_reconstruction

Instruction and scripts for reconstructing ancestral genome from pairwise syntenic blocks using MLGO

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

bioscripts

several scripts for bioinformatics

finder

A fully automated gene annotator from RNA-Seq expression data

haplotypetools

A toolkit for identifying recombination and recombinant genotypes

jarvis

JARVIS, a system to connect LLMs with ML community. Paper: https://arxiv.org/pdf/2303.17580.pdf

kmer-based-subgenome-mapping

learngit

pandas-ai

Pandas AI is a Python library that integrates generative artificial intelligence capabilities into Pandas, making dataframes conversational

pyecharts

🎨 Python Echarts Plotting Library

repeatmasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.

se-mei

Tools for finding mobile element insertions from single-end datasets

subphaser

Phase and visualize subgenomes of an allopolyploid or hybrid based on the repetitive kmers.

t2tools

toney823

trackposon

Pipeline to detect transposable elements (TEs) insertions polymorphism

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

vcf2pcacluster

A new simple and efficient software to PCA and Cluster For popolation VCF File

wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes

yxk_usefull_tools

A simple python package for the beginner of Bioinformatics