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synvisio

SynVisio is an interactive multiscale visualization tool that lets you explore the results of McScanX a popular synteny and collinearity detection toolkit.

syri

Synteny and Rearrangement Identifier

table2itol

Generating iToL annotations from Spreadsheet or CSV files

taxaassign

Pipeline to annotate sequences at different taxonomic levels using NCBI's taxonomy

teloclip

Filter SAM file for soft-clipped alignments containing unassembled telomeric repeats.

tesorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

testb

this is a test

tmerge

Merge transcriptome read-to-genome alignments into non-redundant transcript models

tn-seq

Analysis pipeline for Tn-seq protocol

toa

TOA (Taxonomy-oriented Annotation) establishes workflows geared towards plant species that automate the extraction of information from genomic databases and the annotation of sequences.

tools

tormes

Making whole genome bacterial sequencing data analysis easy

trackplot

Generate IGV style locus tracks from bigWig files in R

treemer

A simple tool to generate hierarchical clustering trees from nucleotide sequences. Supports a number of distance metrics and clustering algorithms. Includes a large testset of SARSCOV2 genomes.

tsebra

TSEBRA: Transcript Selector for BRAKER

tsrfinder

A tool for tRNA-derived small RNA annotation

tutorials

Tutorials on phylogenetic and phylogenomic inference

variantvisualization.jl

Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:

vcf2circos

python plotly Circos from VCF

vcf2dis

VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

vcf2primer

Extract variants from the vcf file and design primers that sandwich the variants.

vcfpop

vennpainter

A tool for the comparison and identification of candidate genes based on Venn diagrams

verkko

vespa

VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

viewbs

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data

wgddetector

wgdi

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

work_flow_of_population_genetics

整理常用的群体遗传学分析流程和脚本