Toney823

EasySpider

A visual no-code/code-free web crawler/spider易采集：一个可视化浏览器自动化测试/数据采集/爬虫软件，可以无代码图形化的设计和执行爬虫任务。别名：ServiceWrapper面向Web应用的智能化服务封装系统。

seqtk

Toolkit for processing sequences in FASTA/Q formats

overpass-turbo

A web based data mining tool for OpenStreetMap using the Overpass API.

goatools

Python library to handle Gene Ontology (GO) terms

omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

NanoPlot

Plotting scripts for long read sequencing data

SpliceAI

A deep learning-based tool to identify splice variants

genomescope

Fast genome analysis from unassembled short reads

rmats-turbo

read2tree

a tool for inferring species tree from sequencing reads

veryfasttree

Efficient phylogenetic tree inference for massive taxonomic datasets

StainedGlass

Make colorful identity heatmaps of genomic sequence

panpop

Application of pan-genome for population

MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

TGG

tomato graph pangenome

DNNGP

DNNGP: Deep neural network for genomic prediction

diploSHIC

feature-based deep learning for the identification of selective sweeps

QuIBL

Quantifying Introgression via Branch Lengths

discoal

discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples

NGS

Scripts for next generation sequencing

bsalign

Banded Striped DNA Sequence Alignment

findGSE

findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model.

NucFreq

ArchaicSeeker2.0

ArchaicSeeker is a series of software for detecting archaic introgression sequences and reconstructing introgression history. The latest version of this series, ArchaicSeeker 2.0, has the following three notable improvements compared with the original version of this software. First, it can automatically determine the boundary of each introgressed sequence. Next, it is capable of tracing both known and unknown ancestral sources of a given introgressed sequence. Finally, it has the ability to reconstruct the introgression history with more sophisticated introgression models.

netviewr

Mutual nearest neighbor graphs for population structure inference and visualization :octopus:

SCASL

single-cell clustering based on alternative splicing landscapes

superSFS

This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot. It is easy-to-use and runing fast. What you should prepare is the phased vcf file containg the data of populations you interested and the outgroup, the outgroup name file, and the annotation file. Enjoy it!!!

GScour

Genome-wide detection of positive selection

Ancestral_Brassicaceae_Karyotype

busco2fasta