SMORE - Synteny Modulator of Repetitive Elements.
This is the readme to the SMORE pipeline, Synteny Modulator Of Repetitive Elements.
Usage: ./SMORE [general_options]
The general options are:
--help|-h print help page --version|-v print version information --citation print citation information --contact print contact information --helpout print explanation for structure and visualization of output files
For subcommands, use: ./SMORE 'subcommand' [options]
The SMORE subcommands are:
bake The subcommand bake combines the subcommands prep and toast in order to easily start and run the pipeline completely. Hence, parameters for bake are the same as the combined parameters for prep and toast. prep This program will sort genetic elements in between genomic anchors based on MultiZ alignments. The genetic elements are taken from a list given as input or retrieved based on a covariance model as input for infernal. toast This program will take the prep-output and calculate the numbers for evolutionary events at the given phylogenetic tree. For a more detailed output, use --verbose or any combination of --clus, --graph, --aln. Please note that the verbose version might take significantly longer. mix This subcommand can be used after running SMORE prep. SMORE mix only produces a list of genetic clusters. This can be used to test different joining methods. Additionally, SMORE mix can split the number of clusters in several disjoint lists such that the succeeding subcommands can be run in parallel on the disjoint subsets to speed up running time of the program for large data sets. In case SMORE mix is splitting the list of clusters, it will output a command list that can be called to continue running the pipeline. The next subcommand to be called is SMORE roast. roast SMORE roast starts from a list of genetic clusters and will output lists of genetic events that can be further proceeded as an input for SMORE eat. SMORE roast can be used for large data sets in order to split and parallelize the process. The next subcommand in the pipeline will be SMORE eat. eat This subcommand is used after SMORE roast and will take list(s) of evolutionary events and output a phylogenetic tree with event and element counts. SMORE eat is able to summarize the outputs of parallelized runs such that all data is recombined at the phylogenetic tree.
For more details, please see the SMORE manual or the SMORE help pages.
For subcommands' help pages: ./SMORE 'subcommand' --help