Command-line tool for de novo identification of LTR retrotransposons.
Basic Local Alignment Search Tool (BLAST):
$ sudo apt-get install ncbi-blast+
- Genome Tools(GT) with enabled HMMER option(with-hmmer=yes) via compilation.
Example install, using VirtualEnv:
# install/use python virtual environment
virtualenv ~/virtenv_scratch --no-site-packages
# activate the virtual environment
source ~/virtenv_scratch/bin/activate
# upgrade pip in the new virtenv
pip install -U pip setuptools
# install this package in DEVELOPMENT mode
python setup.py develop
# or simply install
# python setup.py install
The list of available options:
- --input
Input *.fasta or *.fa file
- --output
Output *.gff file
Option | Description | Default |
---|---|---|
--algorithm | Algorithm, [kmporiginal] | original |
--pattern_len | Length of pattern | 20 |
--min_distance | Minimal distance between LTRs | 1000 |
--max_distance | Maximal distance between LTRs | 20000 |
--min_ltr_len | Minimal length of LTRs | 100 |
--max_ltr_len | Maximal length of LTRs | 1000 |
- --verbose
Include more details
- --debug
Turn on debugging output, do not catch exceptions
See findltr --help
for complete list of available options.