Man pages for carolinafishes/toast
Transcriptome Ortholog Alignment Sequence Tools
| compile_busco_summaries | Get Busco scores from a series of summary files |
| csv2Fasta | Convert a CSV or dataframe with sequences in a column into a... |
| EntrezDownload | Download Public Sequence Data |
| extractBuscos | Utility for extracting BUSCO sequences into individual fasta... |
| extractBuscoSeqsComp | Utility for extracting complete BUSCO sequences into... |
| extractBuscoSeqsDup | Utility for extracting duplicated BUSCO sequences into... |
| extractBuscoSeqsFrag | Utility for extracting fragmented BUSCO sequences into... |
| extractSequences | Utility function for extracting sequences from HMMer outputs |
| FastaIntoPhy | Utility for turning fasta file into phylip file |
| filterOverlappingDomains | Utility for cleaning up HMM scan results |
| geneTreeFilter | Utility for filtering genetrees based on ingroup monophyly or... |
| HMMScanParse | Utility for parsing HMMScan and retrieving domain sequences |
| MafftOrientAlign | Align BUSCO Orthologs |
| MissingDataTable | Utility for Assessing Missing Data in a Set of FASTA Files |
| MissingStreambar | Assess Data Coverage Across All Loci and Taxa |
| NexIntoFas | Utility for turning TOAST superalign.txt into Nexus file |
| ParseScores | Get Busco scores from summary file |
| PartitionTable | Utility for Creating a Partition Table from Fasta Alignments |
| PhyIntoFasta | Utility for turning phylip file into fasta file |
| PhyIntoNex | Utility for turning TOAST superalign.txt into Nexus file |
| PhyloMissmap | Utility for turning TOAST superalign.txt into Nexus file |
| PlotBuscoSummaries | plot Busco scores from the compile_busco_summaries output |
| SuperAlign | Utility for Creating a concatenated alignment from Fasta... |
| ThresholdDataTable | Utility for retrieving species sequences givin a missing data... |
| ThresholdExtract | Utility for retrieving species sequences givin a dataframe of... |
| ToastGoSlim | Assign Go_Slim IDs to BUSCO IDs |
| VisualizeCoverage | Explore Global Patterns of Missing Data |
| VisualizePBR | Explore Global Patterns of Missing Data |
| VisualizeTaxonomyInteractive | Explore Missing Data Interactively Based on a Hierarchical... |
| VisualizeThreshold | Determine and Appropriate Missing Data Threshold |
