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homblocks website  

  HomBlocks is a new and highly efficient pipeline that used homologous blocks searching method to construct multi-gene alignment. It can automatically recognize locally collinear blocks (LCB) among organelle genomes and excavate phylogeny informative regions to construct multi-gene involved alignment in few hours.   Because the traditional way of constructing multi-gene alignments, which was utilized in organelle phylogenomics analysis, is a time-consuming process. Therefore, for the purpose of improving the efficiency of sequence matrix construction derived from multitudes of organelle genomes, we developed a time-saving and accurate method that would be utilized in phylogenomics studies.   In this pipeline, the core conserved fragment (conserved coding genes, functional non-coding regions and rRNA) will be picked out and integrated into a long sequence from the same genome. This method avoids the bothering sequence alignment procedure of every single gene and can generate phylogeny informative and high quality data matrix. Usually, instead of week-long manual work, it only takes less than an hour to construct the HomBlocks matrix with around two dozens of organelle genomes. In addition, HomBlocks produces optimal partition schemes of sequences and sequence evolution models for RAxML, which are important in downstream phylogeny analysis.

Environment Modules

Run module spider homblocks to find out what environment modules are available for this application.

System Variables

  • HPC_HOMBLOCKS_DIR - installation directory
  • HPC_HOMBLOCKS_BIN - executable directory
  • HPC_HOMBLOCKS_DOC - documentation directory
  • HPC_HOMBLOCKS_EXE - example plant directory


If you publish research that uses homblocks you have to cite it as follows:

Guiqi Bi, Yunxiang Mao, Qikun Xing, Min Cao , HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching, Genomics (2017), doi: 10.1016/j.ygeno.2017.08.001