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Multiple sequence alignment

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Name Description Sequence Type* Alignment Type** Link Author Year License ABA A-Bruijn alignment Protein Global download B.Raphael  et al. 2004 Proprietary, without charge for educational, research and non profit. ALE manual alignment ; some software assistance Nucleotides Local download J. Blandy and K. Fogel 1994 (latest version 2007) GPL2 AMAP Sequence annealing Both Global server A. Schwartz and L. Pachter 2006 anon. fast, optimal alignment of three sequences using linear gap costs Nucleotides Global paper   software D. Powell, L. Allison and T. I. Dix 2000 BAli-Phy Tree+Multi alignment ; Probabilistic/Bayesian ; Joint Estimation Both Global WWW+download BD Redelings and MA Suchard 2005 (latest version 2015) GPL Base-By-Base Java-based multiple sequence alignment editor with integrated analysis tools Both Local or Global download R. Brodie  et al. 2004 Free, requires registration. CHAOS/DIALIGN Iterative alignment Both Local (preferred) ...
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Pairwise alignment

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Name Description Sequence Type* Alignment Type** Link Author Year ACANA fast heuristic anchor based pairwise alignment Both Both download Huang, Umbach, Li 2005 AlignMe Alignments for membrane protein sequences Protein Both download , server M. Stamm, K. Khafizov, R. Staritzbichler, L.R. Forrest 2013 Bioconductor Biostrings::pairwiseAlignment Dynamic programming Both Both + Ends-free site P. Aboyoun 2008 BioPerl  dpAlign Dynamic programming Both Both + Ends-free site Y. M. Chan 2003 BLASTZ,LASTZ Seeded pattern-matching Nucleotide Local download , download Schwartz  et al. [9] [10] 2004,2009 DNADot Web-based dot-plot tool Nucleotide Global server R. Bowen 1998 DOTLET Java-based dot-plot tool Both Global applet M. Pagni and T. Junier 1998 FEAST Posterior based local extension with descriptive evolution model Nucleotide Local site A. K. Hudek and D. G. Brown 2010 G-PAS GPU-based dynamic programming with backtracking Both Local, SemiGlobal, Global site+download W. Fr...
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Template search, fold assignment:- PDB-Blast BLAST FastA DALI PhD, TOPITS THREADER 123D UCLA-DOE PROFIT MATCHMAKER 3D-PSSM BIOINGBGU FUGUE LOOPP FASS SAM-T99/T98
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