Prequal REST

PREQUAL

PREQUAL (PRE-alignment QUALity filter) provides a command line tool for examining a group of homologous sequences and filter (remove or mask) characters or stretches within individual sequences that are unlikely to share a common ancestor (homology) with any other character in any other sequence in the group. In practice this filtering targets stretches of the sequences that could be considered a sequence specific insertion, including sequencing errors, inversions, frameshifts, and anything else that means that any stretch of sequence has no simple homology with a stretch in any other sequence. PREQUAL works on unaligned sequences, in other words it filters sequences before multiple sequence alignment. It uses a sophisticated probabilistic modelling approach that does not assume any fixed sequence alignment. PREQUAL works with amino acid sequences, but can also handle DNA sequences of protein-coding genes.

toolId=PREQUAL_XSEDE

Supported parameters:

input.infile_ - Primary Input File
input.specify_TaxonNames_ Select a file that contains a list of taxa names that will not be filtered (-nofilterlist)
input.specify_WordsSeqs_ Number of high posterior residues at beginning and end of core region (-corerun)

vparam.runtime_ - Float - Maximum Hours to Run default=1.0, max = 72

Core options
vparam.specify_NoCore_ (Switch) Do not define a core region (-nocore) default=0.
vparam.specify_HighPosterior_ (Integer) Number of high posterior residues at beginning and end of core region (-corerun) default=3.
vparam.specify_RemoveAll_ (Switch) Remove all residues rather than those outside the core region (-removeall)
vparam.specify_NoMoverepeats_ (Switch) Do not remove repeated regions of length >20 (-noremoverepeat)

Prior and Posterior options

vparam.specify_PPAlgorithm_ (Excl) Number of closest relatives (all|closest|longest) default=closest
vparam.specify_Closest_ (Integer) Compare each sequence of how many closest sequences? Default=10
vparam.specify_Longest_ (Integer) Compare each sequence of how many longest sequences? Default=10
vparam.specify_FilterProp_ (Float) Fraction of the sequences are maintained. (-filterprop) (between 0 and 1)
vparam.specify_FilterThresh_ (Float) Postrerior probability threshold (-filterthresh) (between 0 and 1)
vparam.specify_FilterJoin_ (Integer) Extend filtering over regions of unfiltered sequence less than (-filterjoin)

Output options
vparam.specify_Outsuffix_ (String) Specify a suffix for output files (-outsuffix)
vparam.specify_Dosummary_ (Switch) Output summary statistics to file (-dosummary)
vparam.specify_DoDetail_ (Switch) Output detailed statistics to file (-dodetail)
vparam.specify_NoPPoutput_ (Switch) Stop outputting the posterior probability matrix (--noPP)

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