lizhizhong1992's repositories
RandomMolR
Random scripts for molecular data edition in R
HybPiper
Recovering genes from targeted sequence capture data
LoReAn
Long Reads Annotation pipeline
krait
An ultrafast tool for genome-wide survey of microsatellites and primer design
treedata-book
:books: a complete reference book for treeio, tidytree and ggtree packages
PLWS
Phylogenomics from Low-coverage Whole-genome Sequencing
ggtreeExtra
:lemon: Add Geom Layers On Circular Or Other Layout Tree Of “ggtree”
LTR_retriever
LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
lositan
Lositan/Mcheza selection detection workbench
Ragout
Chromosome-level scaffolding using multiple references
DemographicInference
Scripts to compare models of divergence using diffusion approximation (dadi)
ENMTools
ENMTools R Package
CAFExp
Version 5 of the CAFE phylogenetics software
admixturePipeline
A pipeline that accepts a VCF file to run through Admixture
GetOrganelle
https://github.com/Kinggerm/GetOrganelle/wiki
enmSdm
Faster, better, smarter ecological niche modeling and species distribution modeling
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
SuperCRUNCH
A bioinformatics package for creating, filtering, and manipulating supermatrices and phylogenetic datasets using GenBank and/or local sequence data.
TREEasy
A tool to infer species tree and phylogenetic network from multilocus data
trait-geo-diverse-ungulates
Comparative analysis of abiotic niches in Ungulates
piranha
Scripts for file processing and analysis in phylogenetics and phylogeography
ngsTools
Programs to analyse NGS data for population genetics purposes
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 single copy nuclear genes;
brownlab-workflow-mcmctree
Tutorial for using MCMCTree as implemented by Brown Lab at SIUC. For divergence time estimation on UCE datasets, for dendrobatid frogs.
bio-pipeline
My collection of light bioinformatics analysis pipelines for specific tasks
Dsuite
Fast calculation of the ABBA-BABA statistics across many populations/species
midas-genomics
Custom code used in "Contrasting signatures of genomic divergence in rapidly speciating crater lake cichlid fishes".