| Calling Sequence
| PASfromMSA(msa)
PASfromMSA(msa,lnM,freq)
|
| Parameters
| | Name | Type | Description |
|
| msa
| MAlignment | multiple sequence alignment |
| lnM
| matrix(numeric) | (optional) log. of a 1-PAM matrix |
| freq
| array(numeric) | (optional) character frequencies |
|
| Return Type
| ProbSeq |
| Synopsis
| Computes the probabilistic ancestral sequence at the root of a
phylogenetic tree over a multiple sequence alignment of probabilistic
sequences. For protein sequences, the global variable
NewLogPAM1 is assumed to describe the amino acid mutation probabilities.
The global variable LogLikelihoods will be assigned
to an array containing the ln of the likelihoods at each position. |
| References
| GM Cannarozzi, A Schneider and GH Gonnet (2007): Probabilistic Ancestral Sequences Based on the Markovian Model of Evolution - Algorithms and Applications, in: D Liberless (editor): Ancestral Sequence Reconstruction, Oxford University Press. |
| Examples
| > seqs := ['AAAR','AARR','VTAARRQQ']:
> msa := MAlign(seqs):;
dimensionless fitting index 1470
> print(msa);;
Multiple sequence alignment:
----------------------------
Score of the alignment: 54.882333
Maximum possible score: 54.882333
Sequence 1 _AAAR___
Sequence 2 __AARR__
Sequence 3 VTAARRQQ
> pas := PASfromMSA(msa):
> print(pas);;
pos Most probable chars
1 V 0.83 I 0.05 L 0.04 A 0.03 T 0.02
2 A 0.70 T 0.25 S 0.03 V 0.01 K 0.00
3 A 1.00 S 0.00 V 0.00 G 0.00 T 0.00
4 A 1.00 S 0.00 V 0.00 G 0.00 T 0.00
5 R 1.00 K 0.00 Q 0.00 A 0.00 S 0.00
6 R 0.97 K 0.01 Q 0.00 A 0.00 L 0.00
7 Q 0.70 E 0.06 K 0.05 R 0.03 A 0.03
8 Q 0.70 E 0.06 K 0.05 R 0.03 A 0.03
|
| See also
| MAlign, MAlignment, PASfromTree, ProbAncestor, ProbSeq, PSDynProg |