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my_script_for_record

old-usefully_sofetware

We often encounter some software download methods change or the original website does not exist. This brings a lot of troubles to our subsequent analysis. So this warehouse will collect those old but usefully software. Welcome to supplement and consult.

parsing-repeatmasker-outputs

Few scripts facilitating the extraction of info from Repeat Masker .out files

passionfruit_genomic_database

phact

This is a phylogeny workflow for batch submission to HPC cluster built with Slurm queue manager

phasepaml

phylogenomics_pipeline

After gene family clusing using Orthofinder, single copy nuclear genes and low copies nuclear genes were used to infer the phlogenies between related taxon, three types of data or algorithms were implemented to achive this goal. the perl script phylogenomics_4dtv.pl inferred the phylogeny using four-fold degenerated sites (4DTvs) of combined singl

plant_annotation_tes

Methods and recipes for Plant Genome Annotation - Transposable Elements

plastaumatic

Automated pipeline for assembly and annotation of plastid genomes

pontederia_cordata_survey

population_genomics_pipline

10.1186/s12915-024-01844-x

postitve_selection_scripts

Scripts used for calculating positive selection in ortholg clusters of genes

public_scripts

collection of bioinformatic scripts

radte

Divergence time estimation in the complex history of gene family evolution

rectchr

Multi-level visualization of genomic statistical variables on rectangular chromosomes

rplots-ngs

R scripts for NGS data visualization

shinycircos2

ShinyCircos plot - 2

simple_script

pipeline and tools for personal use

syllabus

synteny_plot_tutorial

telomeres_and_centromeres

This is a method to find telomeres and centromeres of plants.

thalia_dealbata-chloroplast

Thalia dealbata chloroplast

tillandsia-compgenomics

All scripts and notes for the Tillandsia Comparative Genomics project

treeshrink

Implementation of the TreeShrink problem

trimmingpipeline

Python pipeline for PBS script creation for trimming RNA-Seq data with rCorrector, BBDuk, and generating FastQC reports

tutorials

Tutorials on phylogenetic and phylogenomic inference

tvbot

Beautify the phylogenetic tree using one Excel sheet only

wengan

An accurate and ultra-fast hybrid genome assembler

wgddetector

zhangwenda

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