Population Data Analysis

XPCLR

The XP-CLR package implements a composite likelihood method for detecting selective sweeps via the differentiation of two populations.

A demo result URL demo

FastXPRR

FastEPRR uses machine learning to estimate recombination rate R(=4Ner) from intraspecific DNA polymorphism data. When estimating R, the finite-site model was employed to analyze cases with a high rate of recurrent mutations. The variance of R estimated by FastEPRR remains slightly smaller than that estimated by the well-known method, LDhat, when the recombination rate is high. Overall, accuracy of FastEPRR is similar to LDhat but requires far less computation time.

A demo result URL demo

iMAAPs

iMAAPs is a powerful tool to estimate multiple-wave population admixed time, which is currently designed to infer the two-way, multiple-wave admixture based on admixture induced LD. This software can deal with genotype data, haplotype data and the data re-coded according to admixture ancestries.

A demo result URL demo

hmmSweep

Inferring selection intensity and allele age through haplotype structure.

A demo result URL demo

tRNAscan-SE

Scan a sequence file for tRNAs

A demo result URL demo

Rfam

Search Rfam database to do ncRNA annotation using Infernal 1.1.2

A demo result URL demo
  • Strategic Priority Research Program of the Chinese Academy of Sciences,Grant No. XDB13000000
    Maintained by BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences.