Enables the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices.
Department of Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
SeqFIRE funding source(s)
Royal Thai Government Scholarship and a graduate student fellowship from Uppsala University; Estonian Science Foundation Mobilitas [MJD99 and GLOTI9020]; the Center of Excellence in Chemical Biology, University of Tartu, Estonia and the Swedish Research Council [2010-2771]