Exporting files for molecular phylogeny programs

SeqVerter was specifically designed to facilitate automatic manipulation of so-called "infiles" for phylogenetic analysis.

  • You may load a set of aligned sequences and using the checkboxes in the Sequence selection list you may export only some of them to a PHYLIP format infile.
  • "Pruning" is a method of testing the stability of tree topology by removing one species from the alignment and rerunning the phylogenetic analysis.  SeqVerter will allow you to quickly prepare a set of "pruned" PHYLIP files through simple clicking on the checkboxes in the File selection list.

The Alignment processing dialog was specifically designed with phylogenetic analysis in mind.

  • Frequently, sequences selected from databases containing many aligned sequences may include contain gaps.  After alignment, columns containing only gaps may be present.  If this option is selected, SeqVerter will remove empty columns and "compress" the alignment.
  • As some phylogenetic programs may not deal well with missing data, you may use this option to remove columns from the alignment columns, where one or more sequences contain gaps.
  • As sequences frequently contain unresolved positions (Ns) and ambiguous positions (e.g., containing IUPAC ambiguity codes such as R, Y, M, etc.) SeqVerter may locate such columns and remove them from the alignment when creating PHYLIP infiles.

In summary, SeqVerter is a useful tool to manipulate data for phylogenetic analysis.