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 |
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