Last modified on 11 October 2011.
Sections on This Page:
- Primary Alignments: our largest and most complete collections of well-aligned sequences.
- Seed Alignments: derived from primary alignments, smaller alignments that have been highly refined; useful starting points for new alignments.
- Specialized Alignments: derived from primary alignments, phylogenetic subsets of the major alignments.
- Pre-Primary Alignments: precursors to primary alignments; more sequences, but parts of the alignment are unrefined (particularly ends of sequences and variable regions).
- rCAD Datasets: Ribosomal RNA datasets, including structure models spanning the Tree of Life, formatted for import into the rCAD database.
- Alignments Used in Specific Analyses: alignments that have appeared in Gutell Lab publications.
Additional Information:
Primary Alignments:
Table 1: Ribosomal RNA Alignments
Table 2: Intron RNA Alignments
Table 3: Transfer RNA Alignments
Alignment (Abbreviation) [Type] |
Non-Mitochondrial tRNA |
Mitochondrial tRNA |
AE2 | GB | alnFA | rawFA | Seqs |
AE2 | GB | alnFA | rawFA | Seqs |
Alanine (A) [Type 1] |
AE2 | GB | alnFA | rawFA | 4,705 |
N/A |
Cysteine (C) [Type 1] |
AE2 | GB | alnFA | rawFA | 890 |
N/A |
Aspartate (D) [Type 1] |
AE2 | GB | alnFA | rawFA | 1,455 |
N/A |
Glutamate (E) [Type 1] |
AE2 | GB | alnFA | rawFA | 1,935 |
N/A |
Phenylalanine (F) [Type 1] |
AE2 | GB | alnFA | rawFA | 7,723 |
N/A |
Glycine (G) [Type 1] |
AE2 | GB | alnFA | rawFA | 2,713 |
N/A |
Histidine (H) [Type 1] |
AE2 | GB | alnFA | rawFA | 1,802 |
N/A |
Isoleucine (I) [Type 1] |
AE2 | GB | alnFA | rawFA | 4,774 |
N/A |
Lysine (K) [Type 1] |
AE2 | GB | alnFA | rawFA | 1,935 |
N/A |
Methionine (M) [Type 1] |
AE2 | GB | alnFA | rawFA | 1,886 |
N/A |
Asparagine (N) [Type 1] |
AE2 | GB | alnFA | rawFA | 1,261 |
N/A |
Proline (P) [Type 1] |
AE2 | GB | alnFA | rawFA | 1,451 |
N/A |
Glutamine (Q) [Type 1] |
AE2 | GB | alnFA | rawFA | 1,230 |
N/A |
Tryptophan (W) [Type 1] |
AE2 | GB | alnFA | rawFA | 803 |
N/A |
Tyrosine (Y1) [Type 1] |
AE2 | GB | alnFA | rawFA | 187 |
N/A |
Seed Alignments:
Specialized Alignments:
Table 1: Ribosomal RNA Alignments
Pre-Primary Alignments:
Table 1: Ribosomal RNA Alignments
Additional subalignments (marked "FUTURE") and filetypes (AE2, GB, rawFASTA) will be available once the CRW Site migrates to its new server (see the front page for details).
Alignment (Abbreviation) |
5S rRNA |
16S rRNA |
23S rRNA |
AE2 | GB | alnFA | rawFA | Seqs |
AE2 | GB | alnFA | rawFA | Seqs |
AE2 | GB | alnFA | rawFA | Seqs |
Bacteria |
N/A |
AE2 | GB | alnFA | rawFA | 172,373 |
N/A |
Actinobacteria |
N/A |
FUTURE | 18,013 |
N/A |
Aquificae |
N/A |
FUTURE | 397 |
N/A |
Bacteroidetes/Chlorobi group |
N/A |
FUTURE | 7,396 |
N/A |
Caldiserica |
N/A |
FUTURE | 11 |
N/A |
Chlamydiae/Verrucomicrobia group |
N/A |
FUTURE | 135 |
N/A |
Chloroflexi |
N/A |
FUTURE | 32 |
N/A |
Cyanobacteria |
N/A |
AE2 | GB | alnFA | rawFA | 2,770 |
N/A |
Deinococcus-Thermus |
N/A |
FUTURE | 239 |
N/A |
Dictyoglomi |
N/A |
FUTURE | 3 |
N/A |
Fibrobacteres/Acidobacteria group |
N/A |
FUTURE | 68 |
N/A |
Firmicutes |
N/A |
AE2 | GB | alnFA | rawFA | 33,658 |
N/A |
Bacilli |
N/A |
FUTURE | 28,385 |
N/A |
Clostridia |
N/A |
FUTURE | 4,007 |
N/A |
Fusobacteria |
N/A |
FUTURE | 362 |
N/A |
Nitrospirae |
N/A |
FUTURE | 161 |
N/A |
Planctomycetes |
N/A |
FUTURE | 418 |
N/A |
Proteobacteria |
N/A |
FUTURE | 85,665 |
N/A |
Alphaproteobacteria |
N/A |
FUTURE | 20,740 |
N/A |
Betaproteobacteria |
N/A |
FUTURE | 16,035 |
N/A |
Delta/Epsilon subdivisions |
N/A |
FUTURE | 4,492 |
N/A |
Deltaproteobacteria |
N/A |
FUTURE | 2,739 |
N/A |
Epsilonproteobacteria |
N/A |
FUTURE | 1,754 |
N/A |
Gammaproteobacteria |
N/A |
AE2 | GB | alnFA | rawFA | 44,118 |
N/A |
Spirochaetes |
N/A |
AE2 | GB | alnFA | rawFA | 1,890 |
N/A |
Synergistetes |
N/A |
FUTURE | 1 |
N/A |
Tenericutes |
N/A |
AE2 | GB | alnFA | rawFA | 1,459 |
N/A |
Thermodesulfobacteria |
N/A |
FUTURE | 12 |
N/A |
Thermotogae |
N/A |
FUTURE | 215 |
N/A |
unclassified Bacteria |
N/A |
FUTURE | 2,057 |
N/A |
environmental samples |
N/A |
FUTURE | 68,123 |
N/A |
rCAD Data Sets in CRW Format:
Alignment (Abbreviation) |
5S rRNA |
16S rRNA |
23S rRNA |
CRW | Seqs | Str |
CRW | Seqs | Str |
CRW | Seqs | Str |
Three Phylogenetic Domains |
CRW |
5355 |
2908 |
CRW |
5762 |
2361 |
CRW |
670 |
0 |
Alignments Used in Specific Analyses:
Reference |
Description |
Alignments |
4A (2003). rRNA Spliceosomal Introns |
SSU rRNA: All Fungi (1434 sequences) |
AE2 | GB |
SSU rRNA: Spliceosomal Intron-Lacking Fungi (1361 sequences) |
AE2 | GB |
SSU rRNA: Spliceosomal Intron-Containing Fungi (73 sequences) |
AE2 | GB |
LSU rRNA: All Fungi (880 sequences) |
AE2 | GB |
LSU rRNA: Spliceosomal Intron-Lacking Fungi (840 sequences) |
AE2 | GB |
LSU rRNA: Spliceosomal Intron-Containing Fungi (40 sequences) |
AE2 | GB |
4B (2001). AA.AG@helix.ends |
SSU rRNA (Bacteria) |
AE2 | GB |
SSU rRNA (Archaea) |
AE2 | GB |
SSU rRNA (Eucarya (Nuclear)) |
AE2 | GB |
SSU rRNA (Eucarya (Chloroplast)) |
AE2 | GB |
SSU rRNA (Eucarya (Mitochondria)) |
AE2 | GB |
LSU rRNA (Bacteria) |
AE2 | GB |
LSU rRNA (Archaea) |
AE2 | GB |
LSU rRNA (Eucarya (Nuclear)) |
AE2 | GB |
LSU rRNA (Eucarya (Chloroplast)) |
AE2 | GB |
LSU rRNA (Eucarya (Mitochondria)) |
AE2 | GB |
4D (2000). Mollusk Mitochondria |
Eleven mollusk sequences, plus Drosophila and Escherichia as reference points. |
GB |
4D (2001). Polytoma Leucoplasts |
16S rRNA sequence alignment (five chloroplasts, E. coli, and a chloroplast consensus). |
GB | PHYLIP |
4D (2003). ITS (Asteraceae) |
Alignment of ITS1, 5.8S rRNA, and ITS2. |
AE2 | GB | Nexus |
4D (2006). Diatom Shape |
Alignment of 181 diatom taxa, plus E. coli and outgroup sequences. |
AE2 | GB | Nexus |
4E (2001). Red Algae / Brown Algae |
604 SSU rRNA sequences. |
AE2 | GB |
452 Group I intron sequences. |
AE2 | GB |
4E (2005). Fungi / Red Algae |
Alignment of fifty Group IE Intron sequences; Nexus file contains analyzed columns only. |
AE2 | GB | Nexus |