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, though it has five different bioLegato interfaces, where sequence data is divided into two interfaces: bldna and blprotein.

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bldna - DNA sequence data

bldna is a bioLegato instance specialized for working with dna 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, specific sections of the alignment can be selected in blocks and used for further analysis.



To launch bldna from the command line, type

bldna

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. Four additional bioLegato interfaces exploiting this feature are described below.

blprotein - protein sequence data




blprotein is a bioLegato instance specialized for working with protein sequence data.  It has the the same kind of sequence canvas as bldna.  blprotein also uses the same methods as bldna for file input.

To launch blprotein from the command line, type

blprotein


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

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


blmarker - Marker Data

blmarker is a bioLegato interface specialized for molecular marker data.

To launch blmarker, type

blmarker



At present, blmarker 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 or absence of a marker band. To read in discrete data, choose File --> Import Phylip Discrete Data.


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

bltree

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