Bookedited by David J. Russell.
Contents:
Dynamic programming / O. Ufuk Nalbantoglu
Heuristic alignment methods / Osamu Gotoh
Objective functions / Haluk Dogan and Hasan H. Otu
Who watches the watchmen? An appraisal of benchmarks for multiple sequence alignment / Stefano Iantorno ... [et al.]
BLAST and FASTA similarity searching for multiple sequence alignment / William R. Pearson
Clustal omega, accurate alignment of very large numbers of sequences / Fabian Sievers and Desmond G. Higgins
T-coffee : tree-based consistency objective function for alignment evaluation / Cedrik Magi ... [et al.]
MAFFT : iterative refinement and additional methods / Kazutaka Katoh and Daron M. Standley
Multiple sequence alignment using probcons and probalign / Usman Roshan
Phylogeny-aware alignment with PRANK / Ari Loytynoja
GramAlign : fast alignment driven by grammar-based phylogeny / David J. Russell
Multiple sequence alignment with DIALIGN / Burkhard Morgenstern
PicXAA : a probabilistic scheme for finding the maximum expected accuracy alignment of multiple biological sequences / Sayed Mohammad Ebrahim Sahraeian and Byung-Jun Yoon
Multiple protein sequence alignment with MSAProbs / Yongchao Liu and Bertil Schmidt
Large-scale multiple sequence alignment and tree estimation using SATe / Kevin Liu and Tandy Warnow
PRALINE : a versatile multiple sequence alignment toolkit / Punto Bawono and Jaap Heringa
PROMALS3D : multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information / Jimin Pei and Nick V. Grishin
MSACompro : improving multiple protein sequence alignment by predicted structural features / Xin Deng and Jianlin Cheng.