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