MSA: Multiple Sequence Alignment

A Post about multiple sequence alignment construction and analysis




http://en.wikipedia.org/wiki/Multiple_sequence_alignment

paper: 2007 recent evolution of multiple sequence alignment programs
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1963500
http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0030123&ct=1



T-Coffee Tree-based Consistency Objective Function For alignment Evaluation (progressive)
http://www.tcoffee.org/

Muscle multiple sequence alignment by log-expectation
http://www.drive5.com/muscle/

Clustalw
http://www.ebi.ac.uk/Tools/clustalw2/index.html

Mafft MSA algorithm based on fast Fourier. transform
http://align.bmr.kyushu-u.ac.jp/mafft/software/source.html

Show how to download and install each
Show how to run each

publish a little perl script that is able to compare the results of all four, for establishing consistency between the four: number of columns in agreement between the submitted msas