Programs

  



  • OrgConv

OrgConv is a small program for gene conversion detection

The source code (v1.1) in C++ can be downloaded from google code and also here. If you are interested in using it but have difficulty to run it, please contact me.

Special thanks to Tane Kim for fixing bugs in previous code.

Citation:

  • Hao W (2010) OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs. BMC Bioinformatics 11: 114. [Pubmed] [Reprint]

  • Hao W and Palmer JD (2009) Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes. Proc Natl Acad Sci U S A 106: 16728-16733. [Pubmed] [Reprint]


      • DiscML

    DiscML is a small R package for the Evolutionary Analysis of Discrete Characters using Maximum Likelihood

    This resulted from Tane Kim's undergraduate directed study project. The R code DiscML_1.0.1.tar.gz. is available here and at CRAN. The R code was tested on a 5-taxon dataset, the gene family pattern file B1_pattern is here, the tree file B1.tre is here, some command samples are here.


    In order to run DiscML, the ape package is required.

    If you notice any bugs and problems, please report them. Thank you.

    Citation:

  • Kim T and Hao W (2014) DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood. BMC Bioinformatics 15: 320. [Pubmed] [Reprint]

    • Supplementary Data

      


  • Kong Y, Ma JH, Warren K, Tsang RS, Low DE, Jamieson FB, Alexander DC, Hao W* (2013) Homologous recombination drives both sequence diversity and gene content variation in Neisseria meningitidis. Genome Biology and Evolution. [Pubmed] [Reprint]
    • The list of 152 nonvertical genes in ST60 of Neisseria meningitidis can be downloaded Here.

  • Xiao S, Nguyen DT, Wu B, Hao W* (2017) Genetic drift and indel mutation in the evolution of yeast mitochondrial genome size. Genome Biology and Evolution. [Pubmed] [Reprint]
    • The alignments of three pairs of mitogenomes are provided. The alignment of Torulaspora delbrueckii (Tde) Y1535 and Y11634 can be downloaded Here.
    The alignment of Torulaspora quercuum (Tqu) XZ-46A and XZ-129 can be downloaded Here.
    The alignment of Naumovozyma castellii (Nca) Y664 and Y12630 can be downloaded Here.
    The R commands used in statistical analysis can be downloaded Here.
    The sequence alignments used to calculate Ka/Ks (Pi(a)/Pi(s)) can be downloaded Here.