Man pages for gschofl/genoslideR
Create and manipulate multiple genome alignments with annotation.
| aggregateAlignment | Generate summaries on sliding windows over an alignment. |
| alignment2Genome | Map alignment positions to genomic positions. |
| alignSegments | Align orthologous genome segments with 'fsa' |
| aln2map | [INTERNAL] Map a alignment ranges to genomes |
| anchors | Access anchor files |
| annotatedAlignment | Construct an 'annotatedAlignment'. |
| annotatedAlignment-class | Construct an 'annotatedAlignment'. |
| annotationList-class | Construct an "annotationList". |
| file_size | Quickly look up the size of a file |
| findAnnotation | Find annotation associated with alignment positions. |
| fsa | Sequence alignment with fsa |
| genome2Alignment | Map genomic positions to alignment positions. |
| genome2Genome | Map genomic positions in one genome to genomic positions in... |
| genoslideR | Genome Alignments and Annotation. |
| glimmer3 | Ab initio genome annotation using glimmer3 |
| has_command | Test if an external executable is available |
| importAlignment | Import a genome alignment |
| importAnnotation | Import annotation information into 'GRanges'. |
| install_genoslider_dependencies | Install external dependencies for genoslideR |
| labels | Access labels |
| linebreak | Format paragraphs |
| make_tree | [INTERNAL] conctruct NJ or BIONJ tree from one or more... |
| map2aln | [INTERNAL] Map a genomic range to the alignment |
| maskSequence | Softmask repeats and low-complexity regions using RepeatScout... |
| mercator | Run mercator to build a homology map and create orthologous... |
| mergeOrthologyMatrix | Merge a list of pairwise orthology matrices into an... |
| minimum | INTERNAL: Map a genomic range to the alignment |
| ncbi_bacteria | Retrieve bacterial genomes from NCBI FTP site |
| orthologyMatrix | Construct orthology matrices |
| plot.OrthoMatrix | Plot an orthology matrix |
| rbh | Find Reciprocal Best Hits using Blat |
| sliceAlignment | Slice genomic ranges from an alignment. |
| sliceGR | [INTERNAL] Slice GRanges from an alignment |
| sliceGRL | [INTERNAL] Slice GRangesList from an alignment |
| strip_ext | Strip file extensions |
| substituteCDSNumbers | Replace CDS indices in an oframe by the corresponding... |
| SysCall | Wrapper for system commands |
