Align: a Mesquite package for aligning sequence data
The Align package provides some basic tools involving alignment of sequence data. You may also wish to consider using the Opal and Opalescent packages for Mesquite.
The Align package contains:
- Tools for manual alignment
- a Move Blocks tool
- a Push Sequence tool
- commands to remove gaps en masse
- Tools for automated alignment
- a Pairwise Aligner tool
- the ability to have a nucleotide matrix realigned to match an amino acid alignment
- the ability to send a block of the matrix to ClustalW or MUSCLE to align
- Various statistics about taxa based about alignments
- the alignment score of a taxon against a reference taxon
- the ratio of the alignment score of a taxon and its reverse complement against a reference taxon; this allows one to quickly detect sequences that are reverse complements of others.