Package: bioLegato
bioLegato - Programmable graphic user interface
Documentation
Developers Web Site
http://www.bioinformatics.org/wiki/Biolegato
Manual page
$doc/bioLegato/bioLegato_man.txt
Javadoc Documentation
$doc/bioLegato/docs
Data
Platforms
:
solaris-sparc, solaris-amd64, linux-x86_64, linux-intel, osx-x86_64
Installation
:
BIRCH
Programs
:
birch - biolegato interface for launching BIRCH programs
BIRCHSettings.py - Change settings for BIRCH
bl_rename.py - Given a series of filenames, replace the target string with newname string
blast2gi.py - Given output from NCBI Blast+ using the -remote option , create a file containing GI numbers of hits listed in the output
blastdbkit.py - Install and update local BLAST databases
blblastout.py - open BLAST output in a viewer or save the file
bldna - biolegato interface for DNA/RNA sequence analysis
BLExtractSubset.py - Extract a subset of sequences from a GDE flatfile
blgeneric - run BioLegato with no menus and no canvas (for demonstration purposes)
BLHelper.py - Set environment variables for BioLegato Helper Applications
blmarker - bioLegato interface for discrete state data (eg. molecular markers)
blnalign - biolegato interface for working with multiple DNA/RNA alignments
blncbi - Graphical query program for NCBI databases
blnfetch - BioLegato interface for retrieving DNA or RNA sequences from NCBI
blpalign - biolegato interface for working with multiple protein alignments
blpfetch - BioLegato interface for retrieving amino acid sequences from NCBI
blprotein - biolegato interface for protein sequence analysis
blreads - Process and analyze DNA sequencing reads
blrevcomp - reverse-complement, reverse or complement a DNA or RNA strand
blsort.py - Sort a BioLegato table
bltable - Simple spreadsheet for generic data
bltree - bioLegato interface for phylogenetic trees
chooseviewer.py - choose a program for viewing a file
ConfirmBox2 - Opens a popup box with a question and Yes and No buttons.
DirChooser2 - Opens a file chooser, and prints the fully-qualified path of the selected directory.
ErrorBox2 - Opens a popup error box with a message and an Okay button.
Gblocks.py - Wrapper to run Gblocks from BioLegato
gstat.py - Calculates amino acid frequencies and other statistics for one or more proteins
guesspairs.py - Given a list of sequencing read files, make a guess as to which pairs of files should be grouped together as left and right read files
MakeCons - Create a consensus sequence from a multiple alignment
ncbiquery.py - Send an Entrez query to NCBI and return the result
OkayBox2 - Opens a popup box with a message and an Okay button.
phylcnv.py - Convert Phylip files to and from other formats
seqfetch.py - Given a set of GI (UID) or ACCESSION numbers , create a file containing the corresponding sequence entries