RTclass1 is a computational tool that assigns an unclassified non-LTR retrotransposon to one of the known clades of non-LTR retrotransposons based on phylogenetic analysis of a reverse
transcriptase (RT) domain protein sequence encoded by this retrotransposon.
Source Code : RTphylogeny.zip
You must install BioNJ, Clearcut, ClustalW2, Inkscape (optional), JAVA, Muscle, Perl Language, Phylip package, NCBI and WU-BLAST in your computer before using this software. Create a directory and unzip RTphylogeny file into this directory.
From the directory you created, The command is : "perl RTclass1/Pipe_RTclass1.pl sequence output bootvalue"
- sequence : the name of your sequence in Fasta format;
- output : the output file;
- bootvalue : the bootstrap threshold (from 0 to 1000; usually 700);
Kapitonov VV, Tempel S, Jurka J Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences. Gene, 2009 Dec 15;448(2):207-13Kapitonov VV, Jurka J A universal classification of eukaryotic transposable elements implemented in Repbase. Nat Rev Genet, 2008 May;9(5):411-2; author reply 414