my $alignment_file = $ARGV[0]; # fasta alignment; reference sequence must appear first my $first_sequence_is_reference = $ARGV[1]; # if 0, includes first sequence in ...

**IMPORTANT**: AXT formatted alignments will be phased out from Galaxy in the coming weeks. They will be replaced with pairwise MAF alignments, which are already available. To try pairwise MAF ...

FASTA is a text-based file format commonly utilised to represent biological sequences (DNA, RNA, or proteins) in single-letter codes. The format was named after the fasta software package by William ...

Here's how to actually validate one. The problem with single-alignment thinking: You run MAFFT or MUSCLE once. Get output. Use it. But an MSA is parameter-dependent: MAFFT --auto myseqs.fasta = one ...