MACSE aligns coding NT sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons. MACSE is hence the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence.
MAFFT (Multiple sequence Alignment based on Fast Fourier Transform)is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <~200 sequences), FFT-NS-2 (fast; for alignment of <~10,000 sequences), etc.
blast2malign is an easy to use script that creates a multiple alignment (relative to the query) from the database hits of a BLAST search. Multiple HSPs from a database sequence are combined or separated depending on their relationship to each other.
multiAlignFree is an R package which intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data.
Bioinformatics. 2013 Nov 1;29(21):2690-8. doi: 10.1093/bioinformatics/btt462. Epub 2013 Aug 29. Multiple alignment-free sequence comparison.
Ren J1, Song K, Sun F, Deng M, Reinert G.
PROBCONS is an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.