bioLegato is a program that launches other programs. When bioLegato is starts up,  it reads a  file called .GDEmenus, specifiyng a set of programs that bioLegato can call, and the menus for setting parameters. BIRCH has .GDEmenus files for four different data types, resulting in four different bioLegato interfaces.

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biolegato - Sequence Data



biolegato is a bioLegato interface specialized for working with sequence data. The sequence canvas is designed as a multiple sequence alignment editor allowing the insertion and deletion of gaps. As an alternative to using the entire alignment, specifc sections of the alignment can be selected in blocks and used for further analysis. To launch biolegato from the command line, type

biolegato

The File --> Open menu can read four types of files: GDE format, GDE flatfile, FASTA and GenBank. Many other sequence formats can be imported using File --> Import Foreign Format.

The GDE flat file format was designed to allow "sequences" to contain plain text. This was originally intended as a commenting feature, but we can take advantage of it for reading many kinds of text data. Three additional bioLegato interfaces exploiting this feature are described below.

dbiolegato - List Data (eg. Accession numbers, TaxID numbers, GI numbers)

The dbiolegato interface is currently under revision and will be available in later releases.


mbiolegato - Marker Data
mbiolegato is a bioLegato interface specialized for molecular marker data.

To launch mbiolegato, type

mbiolegato

At present, mbiolegato can read marker data in Phylip Discrete Data format or from comma-separated value (.csv) files, as generated from a spreadsheet. This format takes 1's and 0's as markers, usually representing presence of absence of a marker band. To read in discrete data, choose File --> Import Phylip Discrete Data.



tbiolegato - Phylogenetic Tree Data
  tbiolegato is a bioLegato interface specialized for phylogenetic tree data. To launch tbiolegato type

tbiolegato

At present, tbiolegato can only read trees in Phylip tree format. To read in a file containing trees, choose File --> Import Trees.