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anastatus_genome_project

Codes for Anastatus genome paper

bio_tools

Useful bioinformatic scripts

branch-length-analysis-for-protein-evolution

Identify rapidly evolving genes by comparing the branch length. It can help us to identify which ortholog had the most amino acid substitutions after divergence from the common ancestor.

erc-pipeline

The pipeline in this repository allows for the generation of evolutionary rate correlations (ERCs). ERCs use a phylogeny-based approach to look for evolutionary signatures of potential protein-protein interaction. Since ERCs can be fairly straightforward to produce, they can be used as an easy method of discovering candidate protein-protein interactions.

genomics-analysis-pipeline

Some useful bioinformatics pipelines for genomics analysis

hyphy-test-for-selection

Hyphy (Hypothesis Testing using Phylogenies) test for selection

kaks_calculator2.0-for-genome-data

Some scripts for calculating dN and dS for all the individual genes in your dataset.

paml-branch-site-model

Run genomic data using branch-site model in PAML to identify positive selected genes

pathway-gene-loss-analysis

Pathway reconstruction and identity gene loss

pipesmrnaseq

A comprehensive pipeline for small RNAseq data analysis

scripts4pteromalusgenome_ye-et-al-2020-mer

Here are some scripts for Pteromalus genome paper.

summary-the-evolutionary-rates-and-expressions-of-go-terms

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