SQUINT: a multiple alignment program and editor.
Matthew Goode,Allen G. Rodrigo +1 more
TL;DR: SUMMARY SQUINT is a sequence alignment tool, and combines both automated progressive sequence alignment with facilities for manual editing, and permits users to view two translations of the same multiple alignment simultaneously.
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Abstract: SUMMARY SQUINT is a sequence alignment tool, and combines both automated progressive sequence alignment with facilities for manual editing. The program imports nucleotide or amino acid sequence multiple alignment files in standard formats, and permits users to view two translations of the same multiple alignment simultaneously. Edits in one view are instantaneously reflected in the other, and the scoring cost of the changes are shown in real-time. Progressive multiple alignments, using a variety of alignment parameters, can be performed on any block of sequences, including blocks embedded in the existing alignment. AVAILABILITY The software is freely available for download at http://www.cebl.auckland.ac.nz
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References
Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
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Da-Fei Feng,Russell F. Doolittle +1 more
TL;DR: A progressive alignment method that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship is described.
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