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ltr-rte-analysis

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.

maxent

Maximum entropy modelling of species geographic distributions.

maya

Maya's Master Thesis

midas-genomics

Custom code used in "Contrasting signatures of genomic divergence in rapidly speciating crater lake cichlid fishes".

mitochondrial-genome-scripts

mo17_genome_assembly

myscripts

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

ngstools

Programs to analyse NGS data for population genetics purposes

olgenie

Program for estimating dN/dS in overlapping genes (OLGs)

par-spanner

A shell wrapper to split an input large FASTA file and then execute NCBI BLAST or HMMscan in parallel

pcadapt

Performing highly efficient genome scans for local adaptation with R package pcadapt v4

pcs_astral

Scripts for automating Partitioned Coalescence Support (PCS) using ASTRAL

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;

phyloscripts

Helper scripts for processing and visualization of phylogenetics datasets

pipipes

piRNA pipeline collection developed in the Zamore Lab and ZLab in UMass Med School

piranha

Scripts for file processing and analysis in phylogenetics and phylogeography

plann

Plann: a command-line application for annotating plastome sequences

pleurodira-biogeo

Repository related to the publication "Phylogeny, biogeography and diversification patterns of side-necked turtles (Testudines: Pleurodira)"

plothicgenome

The tools are used for displaying hic signal of genome

plws

Phylogenomics from Low-coverage Whole-genome Sequencing

popphylabc

Scripts used for ABC analysis with homo- and heterogeneity in Migration rates or/and Effective population sizes

population-genomics-via-rnaseq

Guide to transcriptome assembly & analysis

populusclimateadaptation

pyscript-bio

生物信息学python代码，专注于重测序文本计算、处理

python_biotrainee

Panda Shen's Python learning scripts

qtlseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis

rad-seq-stacks

radseq

Collection of Python scripts for parsing/analyses of RAD-seq data