The multi-aligner from fransua

multi-aligner's Introduction

Reads sequences from file fasta format, and align them. 
If input sequences are nucleotidic translate them using a given genetic code,
aligns amino-acids sequences, and revert alignment to nucleotide sequences.

Alignment:
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Can use all of these aligners (if available on your computer):
  * muscle (1)
  * mafft (2)
  * dialign-tx (3)
  * probcons (4)

Also gives the option to align inverted sequences.

Masking:
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Once generated your alignments, you can merge them with t-coffee (5). 
Also a cut-off can be applied here, in order 
to mask unstable regions of the alignment 
 -> Mask, here consists in replacing codons by "nnn" (lower case)

Clean alignments with trimal (6), but do not remove poorly aligned columns, it also
masks them, this time "NNN" (upper case).

Rreferences:
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 (1) Edgar R C 2004 
     MUSCLE: multiple sequence alignment with high accuracy and high throughput. 
     Nucleic acids research 32 1792–7
 (2) Katoh K, Kuma K-ichi, Toh H and Miyata T 2005 
     MAFFT version 5: improvement in accuracy of multiple sequence alignment. 
     Nucleic acids research 33 511–8
 (3) Subramanian A R, Kaufmann M and Morgenstern B 2008 
     DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. 
     Algorithms for molecular biology : AMB 3 6
 (4) Do C B, Mahabhashyam M S P, Brudno M and Batzoglou S 2005 
     ProbCons: Probabilistic consistency-based multiple sequence alignment. 
     Genome research 15 330–40
 (5) Notredame C 2010 
     Computing multiple sequence/structure alignments with the T-coffee package. 
     Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] Chapter 3 Unit 3.8.1–25
 (6) Capella-Gutiérrez S, Silla-Martínez J M and Gabaldón T 2009 
     trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. 
     Bioinformatics (Oxford, England) 25 1972–3

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