Phylemon propose 4 alignment tools:

Note: check the compatibility of sequence file format with the alignment tool. The most common is FASTA format, it will be recognize by all tools here.

ClustalW is probably one of the most popular software for alignments. It is a general purpose multiple sequence alignment program for DNA or protein sequences. Most of the options available for users in the command line are here in clickable menus.

You can get more information here ClustalW Documentation

Muscle, a computer program for creating multiple alignments of protein or DNA sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a profile function – “the log-expectation score” – and refinement using tree-dependent restricted partitioning. The inclusion of an iterative alignment refining step, makes it more accurate than Clustal.

You can get more information here Muscle Documentation

Lagan for pairwise alignment of long genomics sequences at any evolutionary distance, performs alignment of sequences using recursive anchoring techniques by means of CHAOS algorithm that works well on distant, as well as related sequences.

You can get more information here Lagan Documentation

M-Lagan for multiple alignment of long genomics sequences at any evolutionary distance, using the same CHAOS algorithm

You can get more information here M-Lagan Documentation

let's try with example:

here a picture of the Muscle page, with the most used options available in the command line version of the program.