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Start Your TrialDivvier is a program intended for the processing of multiple sequence alignments (MSA) before downstream analysis. It was primarily developed for
phylogenetic inference, but the core concepts might be applicable to any application where statistical evidence of shared ancestry is important. The manual should
provide an overview of the methodology – including its strengths and weaknesses – and how to apply it to your data.
use toolid = DIVVIER_XSEDE
Command line options:
input.infile_ - The main input file. This is the same format as IMa2 and Ima2p.
User Configurable Parameters.
vparam.runtime_ (Float) Maximum Hours to Run (up to 168 hours)
vparam.divv_orpartia_ (Excl) Select the algorithm (divvy (default) or partial)
vparam.divvy_threshold_ (Float) Set the divvy threshold (--thresh) between 0 and 1; default=0.801
vparam.partial_threshold_ (Float) Set the partial threshold (--thresh) between 0 and 1; default= 0.774
Approximation options:
vparam.specify_minchars_ (Integer) Minimum number of characters tested in a split (-approx)default=10
vparam.specify_checksplit_ (Switch) Ensure there is a pair for every split (-checksplits) default=0
vparam.specify_HMMexact_ (Switch) Do the full pairHMM and ignore bounding (-HMMexact) default=0
Output options:
vparam.specify_mincolumns_ (Integer) Minimum number of characters in a column to output when divvying/filtering (-mincol) default=2
vparam.output_gap_ (Switch) Output a gap instead of the static * character (-divvygap) default=1