Sentence examples for alignment editing from inspiring English sources

Additional sequences were selected in the database and exported to the sequence alignment program Bioedit [46] for additional alignment editing.

The parenthesized numbers show the change of sequence counts after alignment editing.

In no case did we observe a change in topology as a result of alignment editing.

This method makes it possible to apply a manual-quality alignment editing to large-scale phylogenetic studies.

Unlike the previous analysis [ 2], in order not to introduce subjective bias, manual alignment editing was minimized.

A tree was reconstructed for the edited and unedited alignments and the trees were compared to ensure that there was no change in topology due to alignment editing.

The concatenated DNA sequences of these 636 genes were aligned using MAFFT [54] and the resulting alignment edited using Gblocks [55] to remove any gaps.

Amino acids were aligned with ClustalW [18] and this initial alignment edited manually in MacClade 4.08 (included as supporting File S1) [19].

For phylogenetic analysis, protein sequences were aligned using C LUSTALX 1.83 [ 33], the alignment edited with G ENEDOC 2.6 [ 34] and the phylogenetic analysis performed in M EGA 3.1 [ 35].

The cladogram estimation was performed under a 95% connection limit and gaps were treated as a 5th state with the alignment edited so that each indel was considered a single mutation.

The topology of the maximum likelihood tree based on the nucleotide alignment edited with Gblocks [ 56] (including 6,839 positions) differs from that based on the alignment edited with ALISCORE only with regard to nodes that are not well supported in any of the trees (Additional file 4).