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  1. PrinTE PrinTE Public

    A Forward Simulation Framework for Studying the Role of Transposable Elements in Genome Expansion and Contraction

    Python 11 4

  2. Kmer2LTR Kmer2LTR Public

    Pipeline to estimate insertion time from highly divergent LTR-RTs. (1) Use kmers to identify LTRs from a library of LTR-RTs. (2) Force global alignment of LTRs. (3) Date with p-dist, JC69, and K2P

    Python 3

  3. window_identity window_identity Public

    Calculates and plots Average Nucleotide Identity (ANI) over sliding windows.

    Python

  4. TEsorter TEsorter Public

    Forked from zhangrengang/TEsorter

    TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

    Pep8

  5. LTR_retriever LTR_retriever Public

    Forked from oushujun/LTR_retriever

    LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.

    Perl

  6. synLTR synLTR Public

    Discovery and characterization of syntenic LTR-RTs for phylogenetic analyses.

    Python