recipe tirmite

Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.



MIT / MIT License



Build profile Hidden Markov Models for Terminal Inverted repeat families (TIR-pHMMs) and map to genomic sequences for annotation of MITES and complete DNA-Transposons with variable internal sequence composition.

package tirmite

(downloads) docker_tirmite



depends biopython:


depends pandas:


depends pymummer:


depends python:




You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install tirmite

and update with::

   mamba update tirmite

To create a new environment, run:

mamba create --name myenvname tirmite

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `tirmite/tags`_ for valid values for ``<tag>``)

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