CAARD:Test
Ancestral Maximum Likelihood (ML) Joint Reconstruction
Comments
Ancestral ML reconstructions were performed using FastML 2.02 (Pupko et al. 2000). The tool generates six outputs:
- Pin; reconstructed ancestral NJ tree in newick format.
- Fin; parental relationship among reconstructed nodes and contemporary sequences.
- Jrof; multiple alignment of contemporary sequences and nodes reconstructed with the Joint method.
- Jpf; joint probability per position and total log likelihood.
- Mrof; multiple alignment of contemporary sequences and nodes reconstructed with the marginal method
- Mpf; marginal probability and total log likelihood
Pin output : Ancestral tree
Fin output: Parental relationship among reconstructed nodes and OTUs
| Name | Father | Distance to father | Sons |
|---|---|---|---|
| Retrosat-2 | N1 | 0.508055 | - |
| Del | N2 | 0.418355 | - |
| Peabody | N2 | 0.549836 | - |
| Tma | N3 | 0.402571 | - |
| Legolas | N4 | 0.242758 | - |
| T32022.14 | N4 | 0.20386 | - |
| N1 | root! | - | Retrosat-2 N2 N3 |
| N2 | N1 | 0.13096 | Del Peabody |
| N3 | N1 | 0.114301 | Tma N4 |
| N4 | N3 | 0.161988 | Legolas T32022.14 |
Jpf output: Joint probability per amino acid position and total Log Likelihood
Jrof output: Ancestral ML Reconstruction Alignment
There are two methods of ancestral reconstruction - Joint and Marginal. In this section, we provide a multiple alignment including both input peptidases and ancestral ML sequences reconstructed using the Joint method.The alignment is available in several formats clicking below the option "Set 1". To build HMM profiles and MRC sequences we removed non-informative amino acid stretches and gaps from several ancestral ML reconstruction analyses You can also retrieve the processed Jrof output, clicking below the option "Set 2". Note however that should you cannot select option 2 is because the output was not processed. {{{jrof_output}}}
Mpf output: Marginal probability per amino acid position and total Log Likelihood
Mrof output: Ancestral ML Reconstruction Alignment
There are two methods of ancestral reconstruction - Joint and Marginal. In this section, we provide a multiple alignment including both input peptidases and ancestral ML sequences reconstructed using the Joint method.The alignment is available in several formats clicking below the option "Set 1". To build HMM profiles and MRC sequences we removed non-informative amino acid stretches and gaps from several ancestral ML reconstruction analyses You can also retrieve the processed Jrof output, clicking below the option "Set 2". Note however that should you cannot select option 2 is because the output was not processed. {{{mrof_output}}}
Models
Sequence Logo
{{{sequence_logo}}}
Sequence logo constructed from the input of the processed Jrof alignment. In every position, each residue is a letter whose height is proportional to its frequency multiplied by the information content of each position measured in bits. Letters are placed such that the most common is at the top.
- Basic residues are represented in red
- Hydrophobic residues in black
- Amino acids frequent in β-turns (G and P) in dark grey
- Small nucleophiles in violet
- Acidic residues in orange
- Acidic-relative amides in green
The logo was constructed using ChekAlign server with the Shannon's algorithm (Shannon 1997) and options "include gaps" and "Correction factor". Gaps are not represented by any symbol but occupy a blank also proportional to its frequency and, for aesthetic reasons, always at the top. Maximum entropy is log221. The alignment gap is considered to be another state or amino acid species.
HMMs
{{{hmms}}}
Pairwise alignment between the MRC sequence and the DTG/ILG template HMM-profile
Cite this site
Llorens, C. Futami, R. Renaud, G. and A. Moya (2009). Bioinformatic Flowchart and Database to Investigate the Diversity of Clan AA Peptidases.Biology Direct, 4:3.