UGENE

• UGENE is free open-source cross-platform bioinformatics software
• It works perfectly on Windows, Mac OS and Linux

Install commands for Linux:

sudo add-apt-repository ppa:iefremov/ppa
sudo apt-get update
sudo apt-get install ugene
sudo apt-get install ugene-non-free

Download all dependencies for linux ready to go from here

Online Tutorial can be found here

1. Multiple sequence alignment
2. Basic sequence operations part 1
3. Working with multiple sequence alignments
4. Creating annotations
5. Annotation qualifiers
6. Querying remote database
7. 3D Structure viewer , multiple structure view and image export
8. Local sequence alignment with Smith-Waterman algorithm
9. Restriction enzymes
10. Large alignments
11. Open Reading Frames
12. Chromatograms viewer and editor
13. Finding DNA repeats
14. Searching for homologs of protein sequence with HMMMER3
15. Finding DNA tandem repeats
16. Compare sequences with dotplots
17. Alignment Editor
18. Phylogenetic trees algorithms
19. Transcription binding sites
20. Profile-to-profile and profile-to-sequence MUSCLE alignments
21. Workflow Designer