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an integrated live Linux distribution for the bioinformatics community




LXtoo is a customized Linux distribution for bioinformatics research. The "LX" is the acronym that stands for LiangXian (浪险) in Teochew language (潮州话), and the "too" part is to indicate that LXtoo is based on Gentoo.
LXtoo is developed using free and open source software (FOSS). It aims to present a fast, flexible, portable, and powerful computing platform, coming with most commonly used bioinformatics software pre-compiled, installed, and configured.
LXtoo is distributed as a LiveCD, and can be booted from the CD without making any changes to the underlying operating system, or can run within the popular VMware environment, in parallel with the host operating system. This makes the system portable and useful for new users to try it out, or for those want to demonstrate software to others. LXtoo can also boot from LiveUSB using UNetbootin to creat bootable LiveUSB, and installing to hard driver is recommended for advanced users.


Features included:

  • High performance computing libraries like FFTW, BLAS, and LAPACK, and several software were configured to support these numerical libraries to improve their performance
  • MPI supported, and included parallel versions of clustalW and Gromacs
  • NCBI tools, including popular Blast program and many other tools from NCBI
  • Complete packages like EMBOSS and SMS2 for sequence analysis
  • Sequence alignment programs like ClustalW and ClustalX
  • Gene finder, like qrna, glimmer and glimmerhmm
  • PCR primers design like Primer3
  • Short read mapping and alignment for next-generation sequencing data like bowtie and bfast
  • miRNA target prediction like PITA
  • RNA secondary structure prediction and comparison like Vienna
  • Molecular structures analysis and visualization tool like Chimera
  • Molecular dynamics like Gromacs
  • Network analytical tools, like Cytoscape and igraph library
  • GO and DO semantic similarity analysis like GOSemSim and DOSE
  • Microarray data processing like TM4 and bioconductor packages
  • MS-based proteomics data processing like MSnbase
  • FDR estimation like qvalue package
  • Statistical computing environment R, with Rstudio and ESS
  • BioPython, BioPerl, BioConductor and other programming tools and libraries
  • Tools for managing bibliographies
  • Integrate effectively into existing networked environments (Ruijie authentication was also incorporated)
and more.


Li-Gen Wang, Guangchuang Yu


For questions related to the usage of various programs included, please consult the documentation or website of those programs. For issues with LXtoo itself, suggestions for new software to include, and bug reports, please feel free to get in touch with me.

Copyright © 2012 by the LXtoo Project

College of Information Science and Technology & College of Life Science and Technology, Jinan University