yexinhai Goto Github PK
Name: Xinhai Ye
Type: User
Company: Zhejiang University
Bio: Parasitoid wasp genomics, Evolution, Bioinformatics, ...
Location: Hangzhou China
Name: Xinhai Ye
Type: User
Company: Zhejiang University
Bio: Parasitoid wasp genomics, Evolution, Bioinformatics, ...
Location: Hangzhou China
Codes for Anastatus genome paper
Useful bioinformatic scripts
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.
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.
Some useful bioinformatics pipelines for genomics analysis
Hyphy (Hypothesis Testing using Phylogenies) test for selection
Some scripts for calculating dN and dS for all the individual genes in your dataset.
Run genomic data using branch-site model in PAML to identify positive selected genes
Pathway reconstruction and identity gene loss
A comprehensive pipeline for small RNAseq data analysis
Here are some scripts for Pteromalus genome paper.
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