Se-Al is a user-friendly software application that enables users to create multiple sequence alignments from both nucleotide and amino acid sequences. Its intuitive interface makes it easy to use, even for beginners. With Se-Al, users can quickly and accurately align sequences for a variety of applications in genetics, biology, and more.
Se-Al is a user-friendly software application designed for creating multiple sequence alignments using nucleotide and amino acid sequences. Although the tool does not offer automatic alignments, it is ideal for preparing input for alignment programs like CLUSTAL and phylogeny reconstruction programs such as PHYLIP and PAUP. The software is especially useful for manipulating DNA/RNA sequences of protein-coding.
One of the outstanding features of Se-Al is its ability to import and export sequences in a range of commonly used formats. NEXUS, PHYLIP, MEGA, NBRF, FASTA, GDE and GDE flat formats are supported, but files that fail to import can be sent for inspection. For nucleotide sequences of protein-coding genes, Se-Al allows users to switch between three modes: nucleotides - edit the alignment at the level of single bases, codons - edit the alignment of codons in any reading frame, and translation - edit the alignment of the inferred amino acids translated using various genetic codes. Shifting reading frames, reversing, and complementation can all be done independently, and undo options are available.
Furthermore, alignments can be edited by selecting a block of sequences and sliding it relative to the other sequences, with gaps opening up behind the block that can be undone, and sequences and labels can be edited in a separate window. Raw sequences can also be copied from other sources, such as GENBANK text files and email, and pasted into this window with spaces, formatting, and non-sequence characters removed automatically. A consensus sequence is displayed above the alignment.
Se-Al is also advantageous with its feature of saving alignments in a binary format, which allows rapid opening and the preservation of any transformations such as reading frames, complementation or translation that have been used. Users can cut, copy, and paste whole sequences or sections of alignment within and between alignment documents, as well as copy and paste between Se-Al and other applications in Nexus format. Sequences, alignments, and regions can be dragged and dropped between windows or to other applications in Nexus format. Se-Al also has a search feature for motifs or regions similar to a given sequence, but it is currently very primitive.
One of the outstanding features of Se-Al is its ability to import and export sequences in a range of commonly used formats. NEXUS, PHYLIP, MEGA, NBRF, FASTA, GDE and GDE flat formats are supported, but files that fail to import can be sent for inspection. For nucleotide sequences of protein-coding genes, Se-Al allows users to switch between three modes: nucleotides - edit the alignment at the level of single bases, codons - edit the alignment of codons in any reading frame, and translation - edit the alignment of the inferred amino acids translated using various genetic codes. Shifting reading frames, reversing, and complementation can all be done independently, and undo options are available.
Furthermore, alignments can be edited by selecting a block of sequences and sliding it relative to the other sequences, with gaps opening up behind the block that can be undone, and sequences and labels can be edited in a separate window. Raw sequences can also be copied from other sources, such as GENBANK text files and email, and pasted into this window with spaces, formatting, and non-sequence characters removed automatically. A consensus sequence is displayed above the alignment.
Se-Al is also advantageous with its feature of saving alignments in a binary format, which allows rapid opening and the preservation of any transformations such as reading frames, complementation or translation that have been used. Users can cut, copy, and paste whole sequences or sections of alignment within and between alignment documents, as well as copy and paste between Se-Al and other applications in Nexus format. Sequences, alignments, and regions can be dragged and dropped between windows or to other applications in Nexus format. Se-Al also has a search feature for motifs or regions similar to a given sequence, but it is currently very primitive.
What's New
Version 2.0 Alpha 11: N/A