multiple sequence alignment and alignment editor

Multiple sequence alignment and alignment editor

Multiple sequence alignment

• ClustalW - Alignment of multiple sequences using the ClustalW algorithm

• MUSCLE - Multiple PROTEIN sequences comparison by log-expectation

• T_COFFEE - multiple sequence alignment

• ProbCons - Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences

• MAFFT - Multiple Sequence Alignment based on fast Fourier transform

http://pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_clustalw.html

http://phylogenomics.berkeley.edu/cgi-bin/muscle/input_muscle.py

http://igs-server.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi

http://probcons.stanford.edu/

http://bioinformatics.uams.edu/mafft/

clustalx

• Clustal X is a new windows interface for the ClustalW multiple sequence alignment program.

• ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/

Alignment editor

• Jalview– http://www.jalview.org/

• Seaview

• CINEMA

seaview

cinema

Another presentation

• Seqlogo– Weblogo: http://weblogo.berkeley.edu/

An example

• gi: 16131769

• gi: 15645143

• gi: 37681200

multiple sequence alignment and alignment editor

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