Last modified on 28 July 2008.
Highlights / Data
Sections on This Page:
- Primary Alignments: our largest and most complete collections of sequences.
- Seed Alignments: smaller alignments that have been highly refined; useful starting points for new alignments.
- Specialized Alignments: phylogenetic subsets of the major alignments.
- Alignments Used in Specific Analyses: alignments that have appeared in Gutell Lab publications.
Additional Information:
Primary Alignments:
Table 1: Ribosomal RNA Alignments
| Alignment (Abbreviation) | 5S rRNA | 16S rRNA | 23S rRNA | |||
|---|---|---|---|---|---|---|
| AE2 | GB | alnFA | rawFA | Seqs | AE2 | GB | alnFA | rawFA | Seqs | AE2 | GB | alnFA | rawFA | Seqs | |
| Archaea (A) | AE2 | GB | alnFA | rawFA | 147 | AE2 | GB | alnFA | rawFA | 788 | AE2 | GB | alnFA | rawFA | 226 |
| Bacteria (B) | AE2 | GB | alnFA | rawFA | 2,637 | AE2 | GB | alnFA | rawFA | 35,998 | AE2 | GB | alnFA | rawFA | 5,947 |
| Chloroplast (C) | AE2 | GB | alnFA | rawFA | 199 | AE2 | GB | alnFA | rawFA | 404 | AE2 | GB | alnFA | rawFA | 442 |
| Eukaryota (E) | AE2 | GB | alnFA | rawFA | 2,845 | AE2 | GB | alnFA | rawFA | 1,937 | AE2 | GB | alnFA | rawFA | 115 |
| Mitochondria (M) | AE2 | GB | alnFA | rawFA | 49 | AE2 | GB | alnFA | rawFA | 899 | AE2 | GB | alnFA | rawFA | 285 |
| Three Phylogenetic Domains (3) | AE2 | GB | alnFA | rawFA | 5,624 | AE2 | GB | alnFA | rawFA | 5,591 | AE2 | GB | alnFA | rawFA | 585 |
| Three Phylogenetic Domains/Two Organelles (T) | AE2 | GB | alnFA | rawFA | 5,868 | AE2 | GB | alnFA | rawFA | 6,389 | AE2 | GB | alnFA | rawFA | 922 |
Table 2: Intron RNA Alignments
| Alignment (Abbreviation) | Intron RNA | |
|---|---|---|
| AE2 | GB | alnFA | rawFA | Seqs | |
| Group IA Introns | AE2 | GB | alnFA | rawFA | 109 |
| Group IB Introns | AE2 | GB | alnFA | rawFA | 201 |
| Group IC1 Introns | AE2 | GB | alnFA | rawFA | 818 |
| Group IC2 Introns | AE2 | GB | alnFA | rawFA | 31 |
| Group IC3 Introns | AE2 | GB | alnFA | rawFA | 984 |
| Group ID Introns | AE2 | GB | alnFA | rawFA | 21 |
| Group IE Introns | AE2 | GB | alnFA | rawFA | 248 |
| Group IIA Introns | AE2 | GB | alnFA | rawFA | 174 |
| Group IIB Introns | AE2 | GB | alnFA | rawFA | 607 |
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:
| Alignment (Abbreviation) | 5S rRNA | 16S rRNA | 23S rRNA | |||
|---|---|---|---|---|---|---|
| AE2 | GB | alnFA | rawFA | Seqs | AE2 | GB | alnFA | rawFA | Seqs | AE2 | GB | alnFA | rawFA | Seqs | |
| Archaea | N/A | AE2 | GB | alnFA | rawFA | 132 | AE2 | GB | alnFA | rawFA | 144 | |
| Bacteria | N/A | AE2 | GB | alnFA | rawFA | 1,266 | AE2 | GB | alnFA | rawFA | 1,681 | |
Specialized Alignments:
Table 1: Ribosomal RNA Alignments
| Alignment (Abbreviation) | 5S rRNA | 16S rRNA | 23S rRNA | |||
|---|---|---|---|---|---|---|
| AE2 | GB | alnFA | rawFA | Seqs | AE2 | GB | alnFA | rawFA | Seqs | AE2 | GB | alnFA | rawFA | Seqs | |
| Archaea | ||||||
| Crenarchaeota | N/A | AE2 | GB | alnFA | rawFA | 105 | N/A | ||
| Euryarchaeota | N/A | AE2 | GB | alnFA | rawFA | 567 | N/A | ||
| Bacteria | ||||||
| Actinobacteria | AE2 | GB | alnFA | rawFA | 55 | AE2 | GB | alnFA | rawFA | 4,510 | N/A | |
| Aquificae | N/A | AE2 | GB | alnFA | rawFA | 308 | N/A | ||
| Bacteroidetes/Chlorobi group | N/A | AE2 | GB | alnFA | rawFA | 280 | N/A | ||
| Chlamydiae/Verrucomicrobia group | N/A | AE2 | GB | alnFA | rawFA | 64 | N/A | ||
| Chloroflexi | N/A | AE2 | GB | alnFA | rawFA | 11 | N/A | ||
| Cyanobacteria | N/A | AE2 | GB | alnFA | rawFA | 388 | N/A | ||
| Deinococcus-Thermus | N/A | AE2 | GB | alnFA | rawFA | 124 | N/A | ||
| Fibrobacteres/Acidobacteria group | N/A | AE2 | GB | alnFA | rawFA | 23 | N/A | ||
| Firmicutes | AE2 | GB | alnFA | rawFA | 125 | AE2 | GB | alnFA | rawFA | 6,556 | N/A | |
| Bacillus/Clostridium group | AE2 | GB | alnFA | rawFA | 71 | N/A | N/A | ||
| Bacilli | N/A | AE2 | GB | alnFA | rawFA | 5,363 | N/A | ||
| Clostridia | N/A | AE2 | GB | alnFA | rawFA | 540 | N/A | ||
| Mollicutes | N/A | AE2 | GB | alnFA | rawFA | 496 | N/A | ||
| Fusobacteria | N/A | AE2 | GB | alnFA | rawFA | 50 | N/A | ||
| Nitrospirae | N/A | AE2 | GB | alnFA | rawFA | 22 | N/A | ||
| Planctomycetes | N/A | AE2 | GB | alnFA | rawFA | 34 | N/A | ||
| Proteobacteria | AE2 | GB | alnFA | rawFA | 165 | AE2 | GB | alnFA | rawFA | 11,200 | AE2 | GB | alnFA | rawFA | 164 |
| Alphaproteobacteria | AE2 | GB | alnFA | rawFA | 50 | AE2 | GB | alnFA | rawFA | 3,172 | N/A | |
| Betaproteobacteria | AE2 | GB | alnFA | rawFA | 28 | AE2 | GB | alnFA | rawFA | 3,254 | N/A | |
| Delta/Epsilon subdivisions | N/A | AE2 | GB | alnFA | rawFA | 707 | N/A | ||
| Gammaproteobacteria | AE2 | GB | alnFA | rawFA | 82 | AE2 | GB | alnFA | rawFA | 3,928 | AE2 | GB | alnFA | rawFA | 78 |
| Spirochaetes | N/A | AE2 | GB | alnFA | rawFA | 666 | N/A | ||
| Thermotogae | N/A | AE2 | GB | alnFA | rawFA | 76 | N/A | ||
| Eukaryota | ||||||
| Acanthamoebidae | N/A | AE2 | GB | alnFA | rawFA | 132 | N/A | ||
| Coccidia | N/A | AE2 | GB | alnFA | rawFA | 125 | N/A | ||
| Entamoebidae | N/A | AE2 | GB | alnFA | rawFA | 17 | N/A | ||
| Giardiinae | N/A | AE2 | GB | alnFA | rawFA | 18 | N/A | ||
| Haemosporida | N/A | AE2 | GB | alnFA | rawFA | 24 | N/A | ||
| Haplosporida | N/A | AE2 | GB | alnFA | rawFA | 10 | N/A | ||
| Heterolobosea | N/A | AE2 | GB | alnFA | rawFA | 29 | N/A | ||
| Litostomatea | N/A | AE2 | GB | alnFA | rawFA | 28 | N/A | ||
| Lobosea | N/A | AE2 | GB | alnFA | rawFA | 58 | N/A | ||
| Parabasalidea | N/A | AE2 | GB | alnFA | rawFA | 68 | N/A | ||
| Perkinsea | N/A | AE2 | GB | alnFA | rawFA | 10 | N/A | ||
| Piroplasmida | N/A | AE2 | GB | alnFA | rawFA | 106 | N/A | ||
| stramenopiles | N/A | N/A | N/A | |||
| Bacillariophyta | N/A | AE2 | GB | alnFA | rawFA | 181 | N/A | ||
| Blastocystis | N/A | AE2 | GB | alnFA | rawFA | 49 | N/A | ||
| Oomycetes | N/A | AE2 | GB | alnFA | rawFA | 19 | N/A | ||
| Trypanosomatidae | N/A | AE2 | GB | alnFA | rawFA | 174 | N/A | ||
| Viridiplantae | N/A | N/A | N/A | Streptophyta | N/A | AE2 | GB | alnFA | rawFA | 2,023 | N/A |
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 |
