T-BAS

Example FASTA file download

Example Nexus backbone alignment file download

MAFFT is an alignment program for nucleotide or amino acid sequences. It is not designed for aligning entire genomes. FASTA files should not have sequences greater than 10,000 residues (DNA or amino acids). This tool uses the --auto option in MAFFT, which automatically selects the best algorithm (L-INS-i, FFT-NS-i, and FFT-NS-2) based on the size of the data.

Periods and spaces are not allowed in the file names.

Align to backbone.

Drop aligned sequence file

Drop FASTA files

If you are aligning sequences for phylogenetic inference and generating reference alignments do not trim; otherwise use light trimming or skip trimming (see Portik and Wiens, 2021)

trimAl limit:

You may want to remove very long sequences if you have some that have more data than the area of interest. Sequences longer than 3 times the median length will be removed.

filter long sequences.

You may want to remove short sequences that may not align well. Sequences shorter than 300 bp will be removed.

filter short sequences.

Annotation:

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Phylogenomic Tools