Man pages for gschofl/genoslideR
Create and manipulate multiple genome alignments with annotation.

aggregateAlignmentGenerate summaries on sliding windows over an alignment.
alignment2GenomeMap alignment positions to genomic positions.
alignSegmentsAlign orthologous genome segments with 'fsa'
aln2map[INTERNAL] Map a alignment ranges to genomes
anchorsAccess anchor files
annotatedAlignmentConstruct an 'annotatedAlignment'.
annotatedAlignment-classConstruct an 'annotatedAlignment'.
annotationList-classConstruct an "annotationList".
file_sizeQuickly look up the size of a file
findAnnotationFind annotation associated with alignment positions.
fsaSequence alignment with fsa
genome2AlignmentMap genomic positions to alignment positions.
genome2GenomeMap genomic positions in one genome to genomic positions in...
genoslideRGenome Alignments and Annotation.
glimmer3Ab initio genome annotation using glimmer3
has_commandTest if an external executable is available
importAlignmentImport a genome alignment
importAnnotationImport annotation information into 'GRanges'.
install_genoslider_dependenciesInstall external dependencies for genoslideR
labelsAccess labels
linebreakFormat paragraphs
make_tree[INTERNAL] conctruct NJ or BIONJ tree from one or more...
map2aln[INTERNAL] Map a genomic range to the alignment
maskSequenceSoftmask repeats and low-complexity regions using RepeatScout...
mercatorRun mercator to build a homology map and create orthologous...
mergeOrthologyMatrixMerge a list of pairwise orthology matrices into an...
minimumINTERNAL: Map a genomic range to the alignment
ncbi_bacteriaRetrieve bacterial genomes from NCBI FTP site
orthologyMatrixConstruct orthology matrices
plot.OrthoMatrixPlot an orthology matrix
rbhFind Reciprocal Best Hits using Blat
sliceAlignmentSlice genomic ranges from an alignment.
sliceGR[INTERNAL] Slice GRanges from an alignment
sliceGRL[INTERNAL] Slice GRangesList from an alignment
strip_extStrip file extensions
substituteCDSNumbersReplace CDS indices in an oframe by the corresponding...
SysCallWrapper for system commands
gschofl/genoslideR documentation built on May 14, 2017, 4:11 p.m.