Assembler vs AssemblyLIGN
(a) MacVector Assembler supports reading and aligned display of trace files from automated sequencing machines as well as normal DNA sequences. AssemblyLIGN only supports plain DNA sequences.
(b) Assembler supports the use of quality values so you have a statistical estimate of the error rates in a sequence. This is also displayed graphically. AssemblyLIGN assumed all residues had an equal probability of error.
(c) Assembler uses the phred, phrap and cross_match algorithms from the University of Washington. These are have become the industry standard for sequence assembly over the last 10 years and were previously only available on UNIX machines. AssemblyLIGN used a proprietary algorithm that was never widely accepted.
(d) Assembler can handle thousands of sequences in an alignment. AssemblyLIGN struggled with more than 100 or so, even when running on a modern machine.
(e) Assembler is much faster than AssemblyLIGN and generates significantly better alignments. Because of the use of quality values, you get a statistical estimate of the likely error rate.
(f) Assembler supports masking of vector sequences using the entire vector. AssemblyLIGN needed to know where your cloning sites were located.
(g) Assembler is tightly integrated into MacVector - you can directly analyze contig consensus sequences from within the assembly window with any MacVector nucleotide analysis algorithm (e.g. Restriction enzymes, open reading frames, BLAST etc). With AssemblyLIGN you had to export the consensus then import into MacVector before you could perform any analysis.
Why is it a separate module?
We have to pay royalties to the University of Washington on every sale that includes the phred, phrap and cross_match algorithms. Rather than charge every MacVector user for these algorithms, whether they have a need for them or not, we adjusted the base list price of MacVector and made the Assembler an option for those users who have a need for Contig Assembly. Users who want the Assembler algorithms get the added functionality at the same price as before, users who do not need Assembler pay a lower price.