Repbase

RTclass1

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.

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Paste a single query protein sequence containing the RT domain here (Fasta format):

Don't enter special characters in the sequence name (space, |, \, /, _, !, #, ...), don't use only a number (like '123') and don't use generic name (like 'L1').

Upload a file containing this protein sequence:

Don't enter special characters in the sequence (space, |, \, /, _, !, #, ...), don't use only a number (like '123') and don't use generic name (like 'L1').

Bootstrap value Threshold:

Options :
Multiple Alignment:
Muscle (best)
Clustal profile alignment (use it in a testing mode only)

Phylogenetic Analysis:
Classification is always based on phylogeny
Classification is based on phylogeny only if the input sequence is <40% identical to any sequence from the RTclass dataset

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);

References:

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):207-13

Kapitonov 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