from pair-wise alignments microsats_alignment_level.py $input1 $separation $out_file1 "2way" $mono_threshold $non_mono_threshold $allow_different_units No Yes sputnik

.. class:: infomark **What it does** This tool uses a modified version of SPUTNIK to fetch microsatellite repeats from the input fasta sequences and extracts orthologous repeats from the sputnik output. The modified version allows detection of mononucleotide microsatellites. More information on SPUTNIK can be found on this website_. The modified version is available here_. ----- .. class:: warningmark **Note** - Any block/s not containing exactly 2 species will be omitted. - This tool will filter out microsatellites based on the user input values for minimum distance and repeat number thresholds. Further, this tool will also filter out microsatellites that have no orthologous microsatellites in one of the species. .. _website: http://espressosoftware.com/pages/sputnik.jsp .. _here: http://www.bx.psu.edu/svn/universe/dependencies/sputnik/