PubMed

A statistical score for assessing the quality of multiple sequence alignments.

Ahola V, Aittokallio T, Vihinen M, Uusipaikka E.

BMC Bioinformatics. 2006 Nov 3;7:484.PMID: 17081313 [PubMed - indexed for MEDLINE]Related articlesFree article

Model-based prediction of sequence alignment quality.

Ahola V, Aittokallio T, Vihinen M, Uusipaikka E.

Bioinformatics. 2008 Oct 1;24(19):2165-71. Epub 2008 Aug 4.PMID: 18678587 [PubMed - indexed for MEDLINE]Related articlesFree article

AL2CO: calculation of positional conservation in a protein sequence alignment.

Pei J, Grishin NV.

Bioinformatics. 2001 Aug;17(8):700-12.PMID: 11524371 [PubMed - indexed for MEDLINE]Related articlesFree article

Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.PMID: 15804354 [PubMed - indexed for MEDLINE]Related articlesFree article

Improvement in the accuracy of multiple sequence alignment program MAFFT.

Katoh K, Kuma K, Miyata T, Toh H.

Genome Inform. 2005;16(1):22-33.PMID: 16362903 [PubMed - indexed for MEDLINE]Related articles

DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment.

Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B.

BMC Bioinformatics. 2005 Mar 22;6:66.PMID: 15784139 [PubMed - indexed for MEDLINE]Related articlesFree article

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ.

BMC Bioinformatics. 2003 Oct 10;4:47.PMID: 14552658 [PubMed - indexed for MEDLINE]Related articlesFree article

Accuracy of structure-based sequence alignment of automatic methods.

Kim C, Lee B.

BMC Bioinformatics. 2007 Sep 20;8:355.PMID: 17883866 [PubMed - indexed for MEDLINE]Related articlesFree article

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.

Pandit SB, Skolnick J.

BMC Bioinformatics. 2008 Dec 12;9:531.PMID: 19077267 [PubMed - indexed for MEDLINE]Related articlesFree article

PROMALS web server for accurate multiple protein sequence alignments.

Pei J, Kim BH, Tang M, Grishin NV.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W649-52. Epub 2007 Apr 22.PMID: 17452345 [PubMed - indexed for MEDLINE]Related articlesFree article

An integrated approach to the analysis and modeling of protein sequences and structures. III. A comparative study of sequence conservation in protein structural families using multiple structural alignments.

Yang AS, Honig B.

J Mol Biol. 2000 Aug 18;301(3):691-711.PMID: 10966778 [PubMed - indexed for MEDLINE]Related articles

The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses.

Nelesen S, Liu K, Zhao D, Linder CR, Warnow T.

Pac Symp Biocomput. 2008:25-36.PMID: 18229674 [PubMed - indexed for MEDLINE]Related articlesFree article

Improving model construction of profile HMMs for remote homology detection through structural alignment.

Bernardes JS, Dávila AM, Costa VS, Zaverucha G.

BMC Bioinformatics. 2007 Nov 9;8:435.PMID: 17999748 [PubMed - indexed for MEDLINE]Related articlesFree article

Statistics of local multiple alignments.

Prakash A, Tompa M.

Bioinformatics. 2005 Jun;21 Suppl 1:i344-50.PMID: 15961477 [PubMed - indexed for MEDLINE]Related articlesFree article

Using CLUSTAL for multiple sequence alignments.

Higgins DG, Thompson JD, Gibson TJ.

Methods Enzymol. 1996;266:383-402.PMID: 8743695 [PubMed - indexed for MEDLINE]Related articles

Detailed protein sequence alignment based on Spectral Similarity Score (SSS).

Gupta K, Thomas D, Vidya SV, Venkatesh KV, Ramakumar S.

BMC Bioinformatics. 2005 Apr 23;6:105.PMID: 15850477 [PubMed - indexed for MEDLINE]Related articlesFree article

Ancestral sequence alignment under optimal conditions.

Hudek AK, Brown DG.

BMC Bioinformatics. 2005 Nov 17;6:273.PMID: 16293191 [PubMed - indexed for MEDLINE]Related articlesFree article

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

Bastien O, Ortet P, Roy S, Maréchal E.

BMC Bioinformatics. 2005 Mar 10;6:49.PMID: 15757521 [PubMed - indexed for MEDLINE]Related articlesFree article

Structure alignment based on coding of local geometric measures.

Chang PL, Rinne AW, Dewey TG.

BMC Bioinformatics. 2006 Jul 14;7:346.PMID: 16842622 [PubMed - indexed for MEDLINE]Related articlesFree article

A weighting system and algorithm for aligning many phylogenetically related sequences.

Gotoh O.

Comput Appl Biosci. 1995 Oct;11(5):543-51.PMID: 8590178 [PubMed - indexed for MEDLINE]Related articles