When you are working with NGS data, whether it is DNA-Seq or RNA-Seq, you will want the best algorithms. For speed, BWA-MEM is able to give you reference-guided alignments with genome sizes up to human genome size and beyond. Despite its speed, it still has a small memory requirement. For a feature-rich program able to deal with regular sequences, spliced sequences, methylation-tolerant alignments, SNP-tolerant alignments, and RNA-I tolerant alignments, then GSNAP is the algorithm of choice. You can build the indexes for these programs, re-use them, or share them with colleagues, saving time and effort when working with large projects. And all without going near the command line.
Better still, Sequencher automatically converts the output SAM file to the more compact BAM file and indexes all without you needing to worry about it. This saves you valuable disk space but also time when loading the file into downstream analyses, such as Variant Calling or Differential Expression analysis, or into the Tablet genome browser.
For researchers looking to compare groups of similar sequences, Sequencher has both Clustal and MUSCLE algorithms for performing Multiple-Sequence Alignment. MUSCLE is also used in Sequencher Connections to produce phylogenetic trees.