15 July 2016, 5:00PM update: some additional issues we are facing


“Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes.” (http://selab.janelia.org/recon.html)

Availability & Restrictions

RECON is available to all OSC users without restriction.

The following versions of RECON are available on OSC systems:

Version Glenn Oakley
1.0.5 X  



On the Glenn Cluster, RECON is accessed by executing the following commands:

module load biosoftw
module load RECON

RECON is a collection of several programs that will be added to the users PATH: imagespread, eledef, eleredef, edgeredef, and famdef.  Also added to the users PATH is recon.pl, which executes each of the aforementioned programs.

Using RAxML

raxmlHPC[-MPI|-PTHREADS] -s sequenceFileName -n outputFileName -m substitutionModel [-a weightFileName] [-b bootstrapRandomNumberSeed] [-c numberOfCategories][-d] [-e likelihoodEpsilon] [-E excludeFileName] [-f a|b|c|d|e|g|h|i|j|m|n|o|p|s|t|w|x] [-g groupingFileName] [-h] [-i initialRearrangementSetting] [-j] [-k] [-l sequenceSimilarityThreshold] [-L sequenceSimilarityThreshold] [-M] [-o outGroupName1[,outGroupName2[,...]]] [-p parsimonyRandomSeed] [-P proteinModel] [-q multipleModelFileName] [-r binaryConstraintTree] [-t userStartingTree] [-T numberOfThreads] [-u multiBootstrapSearches] [-v][-w workingDirectory] [-x rapidBootstrapRandomNumberSeed][-y][-z multipleTreesFile] [-#|-N numberOfRuns]


Not currently available.

Further Reading

Fields of Science: