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1. Sequence viewer
2. Creating distance matrices
3. Creating phylogenetic trees
4. Tree viewer
5. Additional features
6. License

## Sequence viewer

• Open and save files in FASTA, NEXUS, PHYLIP, MEGA, CLUSTAL, Stockholm, GDE, NBRF formats (File formats).
• Alignment using MUSCLE. Additional arguments can be provided.
• Drag a selected region to manually align sequences.
• Remove sequences using keyboard.
• Add sequences by opening an other file or dropping a file on the current alignment.
• Copy and paste sequences between Seqtoron and text file editors in NEXUS format.
• Concatenate sequences by opening an other file or dropping a file on the current alignment (sequences must have the same name).
• Unlimited undos/redos.
• Translate temporarily or permanently nucleotide sequences. Nucleotide sequences can be edited while temporarily translated.
• Multiple coloring schemes.
• Keywords search in sequences and sequence names.
• Reverse and complement of sequences.
• 18 genetic codes.
• Increase/decrease font size.
• Seqotron can spell out a selected sequence (Speech function).
• Quick preview of an alignment.

## Creating distance matrices

Compute distance matrices using different distance methods:

• Nucleotide: raw distance, Juke Cantor (JC69), and Kimura 2 Parameter (K2P).
• Amino acid: raw distance, K83.

## Creating phylogenetic trees

Phylogenetic trees can be created using the following methods:

• Distance methods: Neighbor-joining and UPGMA
• Maximum likelihood: Nucleotide (JC69, K80, HKY, GTR) and amino acid (Dayhoff, LG, WAG) models.
• Topology reliability: Bootstrapping and jackknifing (remove one site at a time).
• Multithreading: Bootstrapping and jackknifing are parallelized using PThreads.

## Tree viewer

• Open and save files in NEWICK and NEXUS formats (File formats).
• Reroot tree by selecting a branch.
• Rotate branches.
• Taxa coloring.
• Standard printing.
• Save tree to PDF.
• Increase/decrease font size of taxa.
• Show bootstrap values or other information contained in branches (e.g. rate).
• Keywords search in taxa names.
• Expand/shrink horizontally and vertically tree.
• Ladderize tree.

## Additional features

• Selecting sequences in the sequence viewer automatically select the corresponding taxa in the tree viewer (if any).
• Selecting taxa in the tree viewer automatically select the corresponding sequences in the alignment viewer (if any).

## License

Seqotron is licensed under the GNU General Public License