Man pages for heibl/polenta
Multiple Sequence Alignment with PASTA and GUIDANCE
| align_part_set | Co-optimal alignments from tree partitions |
| centroidDecomposition | Centroid Decomposition of Phylogenetic Trees |
| confidence.heatmap | Plot heatmap of cofidence on MSA |
| decomposePhyloRooted | Decompose Phylogeny |
| deleteGaps | Remove Gap Positions From DNA Sequences |
| equalSubtrees | Split Phylogeny Equally |
| extractMSA | Extract Sequences from POLENTA Output |
| filterMSA | Filtering of the base MSA using polenta scores |
| guidance | MSA Reliability Assessment with GUIDANCE |
| guidance2 | MSA Reliability Assessment with GUIDANCE2 |
| guidanceSA | Interface to guidance program |
| HoT | Heads or Tails Alignment Reliability |
| Hot_GUIDANCE2 | XXX |
| msaBP | Bootstrap a Multiple Sequence Alignnment |
| msaBP_nj_tree | Neighbor joining BP Tree from MSA |
| msa_set_scoreR | Compare reference MSAs with alternative MSAs |
| msa_set_scoreSA | Compare Reference MSAs with Alternative MSAs |
| partitions | Create N-3 Partitions from Phylogeny |
| pasta | Ultra-Large Multiple Sequence Alignment with PASTA |
| polenta | polenta: PASTA Optimal confidENce Transivitiy Alignment |
| polentaAA | Create Objects of Class "polentaAA" |
| polentaAA-class | An S4 Class to represent Amino Acid Alignments with Quality... |
| polenta_dev | Ultra-Large Multiple Sequence Alignment with PASTA |
| polentaDNA | Create Objects of Class "polentaDNA" |
| polentaDNA-class | An S4 Class to represent DNA Alignments with Quality Scores |
| reappendScores | Reappend Scores after Merging |
| reappendScores_dev | Reappend Scores after Merging |
| reappendScores_gen_dev | Reappend Scores after Merging |
| rev_DNA | Reverse DNA Sequences of class DNAbin or AAbin |
| scores | Score Calculation |
| spanningTree | Spanning Tree for PASTA |
| transitivityMerge | Transitivity Merge |
