BioLegato: A General Purpose, Programmable Graphic Interface Alvare, G., Roche-Lima, A. & Fristensky, B. BioLegato: a programmable, object-oriented graphic user interface. BMC Bioinformatics 24, 316 (2023). https://doi.org/10.1186/s12859-023-05436-4

Aug. 30, 2023

BioLegato is best thought of as a program that runs programs. To perform a task on any sequence or other data, simply click or drag on the sequence(s), and choose a program from one of the menus. Each menu button opens a pull-down containing a list of programs. Menus group programs by topic. BioLegato overview Running large jobs	blpalign is one of many BioLegato interfaces. blpalign organizes tasks for protein alignments. BioLegato interfaces exist for DNA and protein sequences, molecular marker data, NCBI keyword queries, BLAST searches, and genome and transcriptome pipelining.
See BioLegato in action on YouTube BIRCH - Desktop Bioinformatics (long version, 38:38) BIRCH - Desktop Bioinformatics (short version, 17:01)

• User Settings
  
• Basic sequence tasks
  
• Working with sequences at the command line
• Working sequences in BioLegato
• Basic shell scripting for sequences
• in-silico PCR of genes using NCBI Primer-BLAST
• Simulated cloning
• Dot-matrix similarity searches
• Pairwise similarity searches
• Annotating and submitting a sequence to GenBank
• Sequence database tasks
• Finding and retrieving sequences from NCBI
• Database similarity searches using BLAST
  
• Database similarity searches using FASTA
  
• Creating datasets of related sequences
• Data pipelining with BioLegato
  
• Multiple sequence alignments
• Phylogenetic analysis
• Distance methods
• Character methods: Parsimony and Maximum Likelihood
• Visualization of Phylogenetic Trees
  
• Discrete state data (0,1)
• Genome visualization with Artemis
• Artemis - basics
  
• DNAPlotter
• Artemis - extracting features from text files
• Comparative Genomics
• Finding and retrieving complete eukaryotic genomes
• Comparing genomes using dotplots
• Comparing genomes using Mauve
• Genome Assembly
• Pre-processing of sequencing reads
• Correction of errors in DNA sequencing reads
• De-novo assembly of genomic seqences
  
• Transcriptome Assembly and Gene Expression
• Pre-processing of RNA sequencing reads
• Correction of errors in RNA sequencing reads
• De-novo transcriptome assembly
• Generating gene expression data from corrected reads
  

Adding features to BioLegato