how to improve multiple sequence alignment by removing outlier sequence ?

Question

[Pei]

Hi all:

Have you tried to remove outlier sequence after constructing a multiple sequence alignment ? Is there any recommended tools for this aim ?

Thanks in advance! Best,

[Khader Shameer]

What type of sequence: protein, nucleotide or others?

Answer 1

[Erik Wright]

Jehl, P., Sievers, F., & Higgins, D. G. (2015). OD-seq: outlier detection in multiple sequence alignments. BMC Bioinformatics, 1–11. http://doi.org/10.1186/s12859-015-0702-1

Answer 2

[Suzanne]

Jalview (www.jalview.org) is a good visualisation workbench for multiple sequence alignments. It has some useful tools for selecting, editing, hiding and grouping sequences, check out this video playlist. When used in combination with the MSA services, it is a great way to interrogate your alignment, as illustrated in this video at about 3.57.