Tools to select sites and sequences that represent variation in a longitudinally sampled protein alignment

Global functions | |
---|---|

CH505 | Man page |

aa.col | Man page |

add.clone | Source code |

annotate.region | Source code |

compute.hd.matrix | Source code |

compute.peak.tf.loss | Source code |

compute.tf.area | Source code |

compute.tf.loss | Source code |

compute.variant.frequencies | Source code |

compute.variant.frequency | Source code |

compute.whenup | Source code |

concatamerize | Source code |

create.refseq.lut | Source code |

create.refseq.lut.from.file | Source code |

create.tf.loss.matrix | Source code |

create.timepoint.parser | Man page Source code |

create_sequence_subset | Source code |

dotify.matrix | Source code |

env.features | Man page |

excise.refseq | Source code |

exclude.vloop.sites | Source code |

export.fasta.swarmset | Man page Source code |

export.swarmset | Man page Source code |

get.refseq.row | Source code |

hamming.dist | Source code |

init.clone.list | Source code |

is.protein | Man page Source code |

lassie | Man page |

lassie-package | Man page |

longest.deletion.per.sequence | Source code |

longest.indel.in.sequence | Source code |

longest.insertion.in.sequence | Source code |

longest.insertion.per.sequence | Source code |

make.logoplot | Source code |

make.swarm.logos | Source code |

make.timepoint.logos | Man page Source code |

onAttach | Source code |

parse.timepoints | Source code |

plot.peak.loss.cdf | Source code |

plot.swarmset | Man page Source code |

plot.swarmtools | Man page Source code |

plot.tf.loss | Source code |

plot.tf.loss.matrix | Source code |

plot.tf.loss.vector | Source code |

plot.variant.frequency | Source code |

pngs2o | Man page Source code |

prep.aln | Man page Source code |

print.swarmset | Man page Source code |

print.swarmtools | Man page Source code |

read.alignment.file | Man page Source code |

report.variant.frequencies | Man page Source code |

resample.swarmset | Man page Source code |

rewrite.custom.colors | Source code |

select.clones | Source code |

select.sites | Source code |

set.alignment | Man page Source code |

set.alignment.file | Man page Source code |

set.excluded.sites | Source code |

set.included.sites | Source code |

set.refseq | Source code |

set.tf | Man page Source code |

set.tf.loss.cutoff | Man page Source code |

set.tp.parser | Man page Source code |

summary.swarmset | Man page Source code |

summary.swarmtools | Man page Source code |

swarmset | Man page Source code |

swarmtools | Man page Source code |

tabulate.swarmset | Man page Source code |

tabulate.variants | Source code |

update.variant.counts | Source code |

vgrepl | Man page Source code |

write.fasta.file | Source code |

write.lut.file | Source code |

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