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  • Genomics
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  • Evolution
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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

How to cite the eGPS

Dalang Yu, Lili Dong, Fangqi Yan, Hailong Mu, Bixia Tang, Xiao Yang, et al. (2019) EGPS 1.0: Comprehensive software for multi-omic and evolutionary analyses. National Science Review, https://doi.org/10.1093/nsr/nwz079