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Removing hits to avoid overlapping HMMs on the same protein sequence.
● Data Source:
CranContrib
● Keywords:
● Alias: hmmerCleanOverlap, nonoverlap
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Computes rarefaction curves for a number of random permutations of genomes.
● Data Source:
CranContrib
● Keywords:
● Alias: rarefaction
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Preparing a FASTA file before starting comparisons of sequences in a pan-genome study.
● Data Source:
CranContrib
● Keywords:
● Alias: panPrep
●
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Generic functions for plotting and printing the content of a Pantree object.
● Data Source:
CranContrib
● Keywords: ~Pantree
● Alias: plot.Pantree, str.Pantree, summary.Pantree
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An extension of the base function gregexpr enabling retrieval of the matching substrings.
● Data Source:
CranContrib
● Keywords: gregexpr
● Alias: gregexpr
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Generic functions for plotting and printing the content of a Binomix object.
● Data Source:
CranContrib
● Keywords: ~Binomix
● Alias: panColor, plot.Binomix, str.Binomix, summary.Binomix
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Generic functions for plotting and printing the content of a Fasta object.
● Data Source:
CranContrib
● Keywords: ~FASTA, ~sequences
● Alias: plot.Fasta, str.Fasta, summary.Fasta
●
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Fits binomial mixture models to the data given as a pan-matrix. From the fitted models both estimates of pan-genome size and core-genome size are available.
● Data Source:
CranContrib
● Keywords:
● Alias: binomixEstimate
●
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The negative truncated log-likelihood function to maximize when fitting binomial mixture models to pan-genome data.
● Data Source:
CranContrib
● Keywords: internal
● Alias: negTruncLogLike
●
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Creates a pan-genome tree based on a pan-matrix and a distance function.
● Data Source:
CranContrib
● Keywords:
● Alias: panTree
●
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providing 
.