Genomics Data Analysis

• Multiple Sequence
  
  Alignment
  To retrieve genomic alignments

• BWA
  
  Burrows-Wheeler-Alignment Tool
  Contributor: Richard Durbin

• BWA-GATK
  
  Variant Discovery in High-Throughput Sequencing Data
  Contributor:Richard Durbin, GATK

• VCFtools
  
  Working with VCF files
  1000 Genomes Project Analysis Group

• CIRI_full
  
  Circular RNA Identification Tool
  Contributor: Fangqing Zhao

• MAP
  
  Model-based analysis of proteomic data
  Contributor: Zhen Shao

Population Data Analysis

• XPCLR
  
  Population differentiation as a test for selective sweeps
  Contributor: Hua Chen

• FastEPRR
  
  Fast & Precise Estimation of Recombination Rate
  Contributor: Haipeng Li

• iMAAPs
  
  Estimation of Multiple-Wave Population Admixed Time
  Contributor: Shuhua Xu

• hmmSweep
  
  Inferring selection intensity and allele age
  Contributor: Hua Chen

• tRNAscan-SE
  
  Searching for tRNA genes in genomic sequence
  Contributor:Todd M. Lowe, Patricia P.Chan

• Rfam
  
  Search Rfam database to do ncRNA annotation using Infernal 1.1.2
  Contributor:Ioanna Kalvari, Anton I. Petrov

Evolution & Network Data Analysis

• Simulator
  
  Demography builder and coalescent-based simulation

• SSN
  
  Sample-Specific Network analysis for disease diagnosis

• iENA
  
  individual-specific Edge-Network Analysis
  Contributor: Luonan Chen

Data Visualization Tools

• Bar Chart
  a package of tools for drawing bar chart

• Bar Brush Chart
  a package of tools for drawing bar brush chart

• Stacked Bar Chart
  a package of tools for drawing stacked bar chart

• Error Bar Chart
  a package of tools for drawing error bar chart

• Line Chart
  a package of tools for drawing line chart

• Graph Force Layout
  a package of tools for drawing graph force layout