PBIL's Tools for Multiple Alignments: http://pbil.univ-lyon1.fr/alignment.html

Multiple Alignment Resource WWW Page (VSNS BioComputing Division): http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html

Multiple Alignment Servers and Software Packages:

MSA: Lipman DJ, Altschul SF, & Kececioglu JD (1989) PNAS 86:4412-4415. Gupta SK, Kececioglu JD, Schaffer AA (1995) J. Comput. Biol. 2:459-472. (http://www.psc.edu/general/software/packages/msa/manual/manual.html )

PIMA: Smith RF & Smith TF (1992) Protein Engng 5:35-41. (Available from the BCM Search Launcher; see below).

Clustal-W: Thompson, JD, Higgins, DG, & Gibson, TJ (1994) Nucleic Acids Res. 22:4673-4680.
ClustalW WWW Server at EBI: http://www.ebi.ac.uk/clustalw
Clustal-W, Clustal-X software packages (Most platforms): ftp://ftp-igbmc.u-strasbg.fr/pub

MAP: Huang, X (1994) CABIOS 10:227-235 (ftp://cs.mtu.edu/pub/huang)

Block Maker: Henikoff S, Henikoff JG, Alford WA, Pietrokovski S (1995) Gene-COMBIS, Gene 163, GC 17-26. (http://blocks.fhcrc.org/blocks)

[MSA, PIMA, Clustal-W, MAP, and Block Maker can be run from the BCM Search Launcher WWW Pages: http://searchlauncher.bcm.tmc.edu]

PRRP/PRRN: Gotoh O (1996). Significant improvements in accuracy of muliple protein sequence alignments by iterative refinments as assessed by reference to structural alignments. J. Mol. Biol. 264:823-838. (http://prrn.ims.u-tokyo.ac.jp/)

DCA: Stoye J (1998). Multiple sequence alignment with the Divide-and-Conquer method. Gene 211:GC45-56 (http://bibiserv.techfak.uni-bielefeld.de/dca/submission.html)

ITERALIGN: Brocchieri L & Karlin S (1998). A symmetric-iterated multiple alignment of protein sequences. J. Mol. Biol. 276:249-264 (http://giotto.stanford.edu/~luciano/iteralign.html)

SAGA: Notredame C, Holm L, Higgens DG (1998). COFFEE: A New Objective Function For Multiple Sequence Alignmnent. Bioinformatics 14:407-422 (http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/saga_home_page.html)

T-COFFEE: Notredame C, Higgins D, Heringa J (2000). T-Coffee: A novel method for multiple sequence alignments. J. Mol. Bio. 302:205-217. (http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html).

SAM-T99: Karplus K, Hu B (2001). Evaluation of protein multiple alignments by SAM-T99 using BALIBASE multiple alignment test set. Bioinformatics 17:713-720. (http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html).

PCMA: Pei J, Sadreyev R, Grishin NV (2003). PCMA: fast and accurate multiple sequence alignment based on profile consistency. Bioinformatics 19:427-428. (ftp://iole.swmed.edu/pub/PCMA/)

ProAlign: Loytynoja A, Milinkovitch MC (2003). A hidden Markov model for progressive multiple alignment. Bioinformatics 19:1505-1513. (http://evol-linux1.ulb.ac.be/ueg/ProAlign/)

MAVID: Bray N, Pachter L (2004). MAVID: Constrained ancestral alignment of multiple sequences. Genome Research 14:693-699. (http://baboon.math.berkeley.edu/mavid)

MUSCLE: Edgar RC (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32:1792-97. (Home Page: http://www.drive5.com/muscle/; Web Server: http://bpg.berkeley.edu/cgi-bin/muscle/input_muscle.py; Use an alignment editor, e.g., Jalview, to view alignment)

Align-m: Walle IV, Lasters I, Wyns L (2004). Align-m -- a new algorithm for multiple alignment of highly divergent sequences. Bioinformatics 20:1428-1435. (binaries: http://bioinformatics.vub.ac.be/software/software.html)

ABA: Raphael B, Zhi D, Tang H, Pevzner (2004). A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Res. 14:2336-46. (Linux binary: http://nbcr.sdsc.edu/euler)

POA: Grasso C, Lee C (2005). Combining partial order alignment and progressive sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics 20:1546-56. (Note: the "POA Online" server appears to be using the older 2002 version of POA: http://www.bioinformatics.ucla.edu/poa/)

DIALIGN-T: Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B (2005). DIALIGN-T: an improved algorithm for seqment-based multiple sequence alignments. BMC Bioinformatics 6:66. (http://dialign-t.gobics.de)

PRALINE-psi: Simossis VA, Kleinjung, Heringa J (2005). Homology-extended sequence alignment. Nucleic Acids Res. 33:816-24. ( http://ibivu.cs.vu.nl/programs/pralinewww/)

MAFFT-5: Katoh K, Kuma K, Toh H, Miyata T (2005). MAFFT version 5: improvement in accuracy of multiple sequence alignment. (binaries & source: http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/)

ProbCons: Do CB, Mahabhashyam MS, Brudno M, Batzpglou S (2005). ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 15:330-40. (http://probcons.stanford.edu)

SPEM: Zhou H, Zhou Y (2005). SPEM: improving multiple sequence alignments with sequence profiles and predicted seconday structures. Bioinformatics 21:3615-21. (Note - server appears to be down at this time: http://theory.med.buffalo.edu/Softwares-Services_files/software-services.htm )

Multiple Alignment Editors/Viewers/Printing Utilities:

Pfaat: Johnson JM, Mason K, Moallemi C, Xi H, Somaroo S, Huang ES (2003). Protein family annotation in a multiple alignment viewer. Bioinformatics 19:544-545. ( http://www.pfizerdtc.com)

QAlign: Sammeth M, Rothganger J, Esser W, Albert J, Stoye J, Harmsen D (2003). QAlign: quality-based multiple alignments with dynamic phylogenetic analysis. Bioinformatics 19:1592-1593. (http://gi.cebitec.uni-bielefeld.de/qalign). Note: This package provides an graphical user interface for a number of multiple alignment programs, including CLUSTALW, DCA, DIALIGN, and T-COFFEE.

Jalview: Clamp M, Cuff J, Searle SM, Barton GJ (2004). The Jalview alignment editor. Bioinformatics 20:426-7. (http://www.jalview.org/index.html).

JAE (Jemboss Alignment Editor): Carver TJ, Mullan LJ (2005). JAE: Jemboss Alignment Editor. Appl. Bioinformatics 4:151-4. (http://emboss.sourceforge.net/Jemboss/).

Also see the list on the PBIL's Tools Page, above.

Misc. Tools To Aid Phylogenetic Analysis:

PhyloBlast: Brinkman F, Wan, I, Hancock R, Rose A, Jones S (2001). PhyloBLAST: facilitating phylogenetic analysis of BLAST results. Bioinformatics 17:385-387. ( http://www.pathogenomics.bc.ca/phyloBLAST/)

RevTrans: Wernersson R, Pedersen A (2003). RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Research 13:3537-3539. ( http://www.cbs.dtu.dk/services/RevTrans/)

RiPE: (Retrieval-induced Phylogeny Environment). Fullen G, Spitzer M, Cullen P, Lorkowski S (2003). BLASTing proteomes, yielding phylogenies. In Silico Biology 3:May 24. (http://ifg-izkf.uni-muenster.de/Bioinformatik/veroeffentlichungen/ripe )