GeneStudio is a multi-purpose sequence analysis suite. Currently, GeneStudio includes three sequence analysis components, SeqVerter, an Alignment editor, and a Contig editor. GeneStudio's modern interface will be familiar to anyone who uses Microsoft Windows software. All GeneStudio components include drag-and-drop file management using GeneStudio's File window, an Entrez interface for retrieving sequences from the NCBI databases, and a BLAST interface for online similarity searches and hit sequence retrieval. GeneStudio components are:
SeqVerter is GeneStudio's free sequence file viewer and conversion utility
- Read and write many popular file formats.
- Open sequences from multiple files in different formats and combine them into new files.
- Data viewers include:
- Sequence file data.
- Raw sequence file.
- Trace data, if any.
- Formatted sequence display for printing or pasting into other applications.
GeneStudio's Alignment editor provides tools for creating and editing multiple sequence alignments, and phylogenetic analysis.
- Create alignments using a graphical interface to CLUSTAL W.
- Edit alignments using the word processor-like editor.
- In addition, the Alignment editor has a convenient interface to phylogenetic analysis programs, such as TREE-PUZZLE, fastDNAml, and selected programs from the PHYLIP package (DNADIST/NEIGHBOR, DNAML, DNAPARS including SEQBOOT and CONSENSE).
- Data viewers include:
- Sequence list provides an editable list of open sequences.
- Pretty view provides a formatted, printable alignment display.
- An interface to the popular TreeView phylogenetic tree display and editing program is also provided.
The Contig editor provides tools for the assembly and editing of sequences from automatic sequencer files.
- Automatic trace file trimming.
- Rapidly locate and edit ambiguous positions with the Ambiguity finder.
- A translation tool provides editing guidance.
- Switch between contigs easily using the drop-down contig list.
- Fold and unfold trimmed ends by dragging the arrow at either end of the sequence.
- Data viewers:
- The Contig editor's Viewers window provides displays of the data.
- The Sequence list is used to select sequences for assembly.
- The Map view provides a graphical view of contig coverage.
- The Trace view provides a printable display of the raw trace data.
- Pretty view provides a formatted, printable display of all sequences in each contig.