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MAlign

Function MAlign - multiple sequence alignment using various methods

Calling Sequence MAlign(seqs,method,labels,tree,allall)

Parameters

Name	Type	Description

`seqs`	list(string)	sequences to align
`method`	string	(optional) method(s) to compute the alignment
`labels`	list(string)	(optional) labels for the sequences
`tree`	Tree	(optional) Tree used by the prob method
`allall`	matrix({0,Alignment})	(optional) all-against-all Alignments

Return Type MAlignment

Globals MSA_CircularTour,

Synopsis MAlign does a multiple sequence alignment (MSA) using the given method(s). The valid methods are:

prob Probabilistic method to build MSA

circ Circular tour method to build MSA

best Chooses the best of 4 methods (expensive)

Global Global alignments between sequences

Local Local alignments between sequences

CFE Cost Free End alignments between sequences

GapHeuristic Use gap heuristics to improve the result

If a method is not specified, the probabilistic method will be used. The GapHeuristic can be specified in addition to the other method specification.

If a tree is not provided, it will be calculated (for the Probabilistic method which needs a tree).

If an all-against-all Alignment array is not provided, one will be calculated. With the method best, 4 different multiple sequence alignments will be computed (circular, and probabilistic with Local, CFE and Global) and the best scoring one will be returned. GapHeuristics are used for the 4 methods. This is naturally 4 times more expensive than a single alignment and should be used with care.

Examples

> msa := MAlign(['ASDFAA','ASDAV','ASFDAA']):;

dimensionless fitting index 73.14

> print(msa);

Multiple sequence alignment:
----------------------------
Score of the alignment: 14.782993
Maximum possible score: 23.171372

Sequence 1    _ASDFAA
Sequence 2    _ASDAV_
Sequence 3    ASFDAA_

> msa := MAlign(['ASDFAA','ASDAV','ASFDAA'], 'circ'):;

> print(msa);

Multiple sequence alignment:
----------------------------
Score of the alignment: 1.8851224
Maximum possible score: 15.639881

Sequence 1    ASDFAA
Sequence 2    ASD_AV
Sequence 3    ASFDAA

See also Align, Alignment, Clusters, DynProgScore, DynProgStrings, MAlignment